From fe52aec22c97cd357d1b6c40c2954d27ebad87d3 Mon Sep 17 00:00:00 2001 From: ramiz khaled Date: Wed, 6 Aug 2025 10:11:30 +0200 Subject: [PATCH 1/7] add: create_assembly_picklists wrapper --- tools/create_assembly_picklists/.shed.yml | 9 + .../CreateAssemblyPicklists_script.py | 588 ++++++++++++++++++ .../create_assembly_picklists.xml | 206 ++++++ .../test-data/emma_parts/HC_Amp_ccdB.gb | 109 ++++ .../test-data/emma_parts/conn a-c.gb | 76 +++ .../test-data/emma_parts/conn b-e.gb | 75 +++ .../test-data/emma_parts/conn b-l.gb | 75 +++ .../test-data/emma_parts/conn d-e.gb | 75 +++ .../test-data/emma_parts/conn d-f.gb | 75 +++ .../test-data/emma_parts/conn h-ha.gb | 80 +++ .../test-data/emma_parts/conn h-j.gb | 80 +++ .../test-data/emma_parts/conn h-k.gb | 80 +++ .../test-data/emma_parts/conn j-k.gb | 75 +++ .../test-data/emma_parts/conn l-n.gb | 76 +++ .../test-data/emma_parts/conn l-r.gb | 76 +++ .../test-data/emma_parts/conn l-w.gb | 76 +++ .../test-data/emma_parts/conn l-y.gb | 76 +++ .../test-data/emma_parts/conn q-r.gb | 76 +++ .../test-data/emma_parts/conn r-w.gb | 75 +++ .../test-data/emma_parts/conn t-v.gb | 79 +++ .../test-data/emma_parts/conn w-x.gb | 76 +++ .../test-data/emma_parts/conn w-y.gb | 76 +++ .../test-data/emma_parts/conn w-z.gb | 76 +++ .../test-data/emma_parts/conn y-z.gb | 76 +++ .../test-data/emma_parts/p10_tet-aptazyme.gb | 75 +++ .../test-data/emma_parts/p11_sv40polya.gb | 74 +++ .../test-data/emma_parts/p14_cmvp.gb | 86 +++ .../test-data/emma_parts/p14_sv40p.gb | 82 +++ .../test-data/emma_parts/p15_puror.gb | 96 +++ .../test-data/emma_parts/p16_bghpolya.gb | 77 +++ .../test-data/emma_parts/p18_cmvp.gb | 86 +++ .../test-data/emma_parts/p18_ef1ap.gb | 98 +++ .../test-data/emma_parts/p19_mneogreen.gb | 98 +++ .../test-data/emma_parts/p19_mruby2.gb | 99 +++ .../test-data/emma_parts/p19_mtagbfp2.gb | 99 +++ .../test-data/emma_parts/p19_tet-on-3g.gb | 95 +++ .../test-data/emma_parts/p1_5'-itr-pb.gb | 78 +++ .../test-data/emma_parts/p1_5'ha-haavs1.gb | 87 +++ .../test-data/emma_parts/p20_ct-minute-nes.gb | 74 +++ .../test-data/emma_parts/p20_ct-nes.gb | 74 +++ .../test-data/emma_parts/p20_linker3.gb | 74 +++ .../test-data/emma_parts/p20_p2a.gb | 80 +++ .../test-data/emma_parts/p21_dmra.gb | 82 +++ .../test-data/emma_parts/p21_mkate2.gb | 90 +++ .../test-data/emma_parts/p21_mneogreen.gb | 92 +++ .../test-data/emma_parts/p21_mruby2.gb | 93 +++ .../test-data/emma_parts/p21_mtagbfp2.gb | 93 +++ .../test-data/emma_parts/p21_puror.gb | 90 +++ .../test-data/emma_parts/p22_pgkpolya.gb | 76 +++ .../test-data/emma_parts/p23_insulatorfb.gb | 74 +++ .../test-data/emma_parts/p24_3'ha_haavs1.gb | 82 +++ .../test-data/emma_parts/p24_3'pb.gb | 76 +++ .../test-data/emma_parts/p25_sv40-ori.gb | 75 +++ .../test-data/emma_parts/p2_insulatorfb.gb | 74 +++ .../test-data/emma_parts/p3_cagp.gb | 86 +++ .../test-data/emma_parts/p3_cmvp_tet.gb | 98 +++ .../test-data/emma_parts/p3_ef1ap.gb | 98 +++ .../test-data/emma_parts/p3_tre3gp.gb | 115 ++++ .../test-data/emma_parts/p4_kt-l7ae -weiss.gb | 72 +++ .../test-data/emma_parts/p4_lac-o.gb | 87 +++ .../test-data/emma_parts/p5_attb-bxb1.gb | 76 +++ .../test-data/emma_parts/p5_attp-bxb1.gb | 77 +++ .../test-data/emma_parts/p5_k1-k1.gb | 75 +++ .../test-data/emma_parts/p5_kt-weiss.gb | 75 +++ .../test-data/emma_parts/p6_atg_boxc.gb | 79 +++ .../test-data/emma_parts/p6_kozak-atg.gb | 76 +++ .../emma_parts/p6_nt-igkl sequence.gb | 83 +++ .../test-data/emma_parts/p6_nt-mls.gb | 81 +++ .../emma_parts/p6_nt-myristoylation signal.gb | 81 +++ .../emma_parts/p6_nt-palm sequence.gb | 81 +++ .../test-data/emma_parts/p6_nt-sv40_nls.gb | 82 +++ .../test-data/emma_parts/p7_bxb1.gb | 107 ++++ .../test-data/emma_parts/p7_l7ae-weiss.gb | 82 +++ .../test-data/emma_parts/p7_l7ae.gb | 87 +++ .../test-data/emma_parts/p7_laci.gb | 98 +++ .../test-data/emma_parts/p7_mcherry.gb | 89 +++ .../test-data/emma_parts/p7_mkate2.gb | 90 +++ .../test-data/emma_parts/p7_mneogreen.gb | 91 +++ .../test-data/emma_parts/p7_mruby2.gb | 93 +++ .../test-data/emma_parts/p7_mtagbfp2.gb | 93 +++ .../test-data/emma_parts/p8_linker1.gb | 75 +++ .../test-data/emma_parts/p8_linker2.gb | 74 +++ .../test-data/emma_parts/p8_p2a.gb | 80 +++ .../test-data/emma_parts/p8a_ct-kdel.gb | 75 +++ .../test-data/emma_parts/p8b_ires2.gb | 84 +++ .../test-data/emma_parts/p9_a-tubulin.gb | 103 +++ .../test-data/emma_parts/p9_bsdr.gb | 82 +++ .../test-data/emma_parts/p9_dmrc.gb | 83 +++ .../emma_parts/p9_firefly luciferase.gb | 120 ++++ .../test-data/emma_parts/p9_mneogreen.gb | 92 +++ .../test-data/emma_parts/p9_mruby2.gb | 93 +++ .../test-data/emma_parts/p9_mtagbfp2.gb | 93 +++ .../test-data/emma_parts/p9_neor.gb | 94 +++ .../test-data/emma_parts/p9_puror.gb | 90 +++ .../test-data/example_echo_plate.xlsx | Bin 0 -> 12225 bytes .../test-data/example_picklist.xls | Bin 0 -> 8192 bytes 96 files changed, 8460 insertions(+) create mode 100644 tools/create_assembly_picklists/.shed.yml create mode 100644 tools/create_assembly_picklists/CreateAssemblyPicklists_script.py create mode 100644 tools/create_assembly_picklists/create_assembly_picklists.xml create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/HC_Amp_ccdB.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/conn a-c.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/conn b-e.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/conn b-l.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/conn d-e.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/conn d-f.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/conn h-ha.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/conn h-j.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/conn h-k.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/conn j-k.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/conn l-n.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/conn l-r.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/conn l-w.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/conn l-y.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/conn q-r.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/conn r-w.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/conn t-v.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/conn w-x.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/conn w-y.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/conn w-z.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/conn y-z.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p10_tet-aptazyme.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p11_sv40polya.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p14_cmvp.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p14_sv40p.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p15_puror.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p16_bghpolya.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p18_cmvp.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p18_ef1ap.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p19_mneogreen.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p19_mruby2.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p19_mtagbfp2.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p19_tet-on-3g.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p1_5'-itr-pb.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p1_5'ha-haavs1.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p20_ct-minute-nes.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p20_ct-nes.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p20_linker3.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p20_p2a.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p21_dmra.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p21_mkate2.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p21_mneogreen.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p21_mruby2.gb create mode 100644 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tools/create_assembly_picklists/test-data/emma_parts/p6_nt-myristoylation signal.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p6_nt-palm sequence.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p6_nt-sv40_nls.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p7_bxb1.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p7_l7ae-weiss.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p7_l7ae.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p7_laci.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p7_mcherry.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p7_mkate2.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p7_mneogreen.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p7_mruby2.gb create mode 100644 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tools/create_assembly_picklists/test-data/emma_parts/p9_mruby2.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p9_mtagbfp2.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p9_neor.gb create mode 100644 tools/create_assembly_picklists/test-data/emma_parts/p9_puror.gb create mode 100644 tools/create_assembly_picklists/test-data/example_echo_plate.xlsx create mode 100644 tools/create_assembly_picklists/test-data/example_picklist.xls diff --git a/tools/create_assembly_picklists/.shed.yml b/tools/create_assembly_picklists/.shed.yml new file mode 100644 index 00000000..1cc96ded --- /dev/null +++ b/tools/create_assembly_picklists/.shed.yml @@ -0,0 +1,9 @@ +name: create_assembly_picklists +owner: tduigou +categories: + - Systems Biology + - Synthetic Biology +description: Provide a source plate map and an assembly plan, get a robotic picklist spreadsheet for Tecan EVO or Labcyte Echo +long_description: Provide a source plate map and an assembly plan, get a robotic picklist spreadsheet for Tecan EVO or Labcyte Echo +homepage_url: https://github.com/Edinburgh-Genome-Foundry/CUBA/blob/master/backend/app/views/create_assembly_picklists/CreateAssemblyPicklistsView.py +remote_repository_url: https://github.com/Edinburgh-Genome-Foundry/Plateo \ No newline at end of file diff --git a/tools/create_assembly_picklists/CreateAssemblyPicklists_script.py b/tools/create_assembly_picklists/CreateAssemblyPicklists_script.py new file mode 100644 index 00000000..c09b821f --- /dev/null +++ b/tools/create_assembly_picklists/CreateAssemblyPicklists_script.py @@ -0,0 +1,588 @@ +#!/usr/bin/env python +# coding: utf-8 +# Code copied from CUBA backend tools.py and create_assembly_picklists/CreateAssemblyPicklistsView.py +# Code modified for running in a script in Galaxy. +############################################################################## +############################################################################## +# App code +## EGF Galaxy Create assembly picklists -- script + +############################################################################## +# IMPORTS +import argparse +import os +from io import StringIO, BytesIO +import re +from base64 import b64encode, b64decode +from copy import deepcopy +import sys + +from collections import OrderedDict +from fuzzywuzzy import process +import matplotlib.pyplot as plt +from matplotlib.backends.backend_pdf import PdfPages +import pandas + +from Bio import SeqIO +from Bio.SeqRecord import SeqRecord +from Bio.Seq import Seq + +import bandwagon as bw +import crazydoc +from dnachisel.biotools import sequence_to_biopython_record +import dnacauldron +import flametree +from plateo import AssemblyPlan +from plateo.parsers import plate_from_content_spreadsheet +from plateo.containers import Plate4ti0960 +from plateo.exporters import AssemblyPicklistGenerator, picklist_to_assembly_mix_report +from plateo.exporters import ( + picklist_to_labcyte_echo_picklist_file, + picklist_to_tecan_evo_picklist_file, + plate_to_platemap_spreadsheet, + PlateTextPlotter, +) +from plateo.tools import human_volume +from snapgene_reader import snapgene_file_to_seqrecord + + +############################################################################## +# FUNCTIONS + +def fix_and_rename_paths(paths): + fixed_paths = [] + for path in paths: + new_path = path.replace("__sq__", "'") + if new_path != path: + os.rename(path, new_path) + fixed_paths.append(new_path) + return fixed_paths + + +def did_you_mean(name, other_names, limit=5, min_score=50): # test + results = process.extract(name, list(other_names), limit=limit) + return [e for (e, score) in results if score >= min_score] + + +def fix_ice_genbank(genbank_txt): + lines = genbank_txt.splitlines() + lines[0] += max(0, 80 - len(lines[0])) * " " + return "\n".join(lines) + + +def write_record(record, target, fmt="genbank"): + """Write a record as genbank, fasta, etc. via Biopython, with fixes""" + record = deepcopy(record) + if fmt == "genbank": + if isinstance(record, (list, tuple)): + for r in record: + r.name = r.name[:20] + else: + record.name = record.name[:20] + if hasattr(target, "open"): + target = target.open("w") + SeqIO.write(record, target, fmt) + + +def autoname_genbank_file(record): + return record.id.replace(".", "_") + ".gb" + + +def string_to_records(string): + """Convert a string of a fasta, genbank... into a simple ATGC string. + + Can also be used to detect a format. + """ + matches = re.match("([ATGC][ATGC]*)", string) + # print("============", len(matches.groups()[0]), len(string)) + # print (matches.groups()[0] == string) + if (matches is not None) and (matches.groups()[0] == string): + return [SeqRecord(Seq(string))], "ATGC" + + for fmt in ("fasta", "genbank"): + if fmt == "genbank": + string = fix_ice_genbank(string) + try: + stringio = StringIO(string) + records = list(SeqIO.parse(stringio, fmt)) + if len(records) > 0: + return (records, fmt) + except: + pass + try: + record = snapgene_file_to_seqrecord(filecontent=StringIO(string)) + return [record] + except: + pass + raise ValueError("Invalid sequence format") + + +def file_to_filelike_object(file_, type="byte"): + content = file_.content.split("base64,")[1] + filelike = BytesIO if (type == "byte") else StringIO + return filelike(b64decode(content)) + + +def spreadsheet_file_to_dataframe(filedict, header="infer"): + filelike = file_to_filelike_object(filedict) + if filedict.name.endswith(".csv"): + return pandas.read_csv(filelike, header=header) + else: + return pandas.read_excel(filelike, header=header) + + +def records_from_zip_file(zip_file, use_file_names_as_ids=False): + zip_name = zip_file.name + zip_file = flametree.file_tree(file_to_filelike_object(zip_file)) + records = [] + for f in zip_file._all_files: + ext = f._extension.lower() + if ext in ["gb", "gbk", "fa", "dna"]: + try: + new_records, fmt = string_to_records(f.read()) + if not isinstance(new_records, list): + new_records = [new_records] + except: + content_stream = BytesIO(f.read("rb")) + try: + record = snapgene_file_to_seqrecord(fileobject=content_stream) + new_records, fmt = [record], "snapgene" + except: + try: + parser = crazydoc.CrazydocParser( + ["highlight_color", "bold", "underline"] + ) + new_records = parser.parse_doc_file(content_stream) + fmt = "doc" + except: + raise ValueError("Format not recognized for file " + f._path) + + single_record = len(new_records) == 1 + for i, record in enumerate(new_records): + name = record.id + if name in [ + None, + "", + "", + ".", + " ", + "", + ]: + number = "" if single_record else ("%04d" % i) + name = f._name_no_extension.replace(" ", "_") + number + record.id = name + record.name = name + record.file_name = f._name_no_extension + record.zip_file_name = zip_name + if use_file_names_as_ids and single_record: + basename = os.path.basename(record.file_name) + basename_no_extension = os.path.splitext(basename)[0] + record.id = basename_no_extension + records += new_records + return records + + +def records_from_data_file(data_file): + content = b64decode(data_file.content.split("base64,")[1]) + try: + records, fmt = string_to_records(content.decode("utf-8")) + except: + try: + record = snapgene_file_to_seqrecord(fileobject=BytesIO(content)) + records, fmt = [record], "snapgene" + except: + try: + parser = crazydoc.CrazydocParser( + ["highlight_color", "bold", "underline"] + ) + records = parser.parse_doc_file(BytesIO(content)) + fmt = "doc" + except: + try: + df = spreadsheet_file_to_dataframe(data_file, header=None) + records = [ + sequence_to_biopython_record(sequence=seq, id=name, name=name) + for name, seq in df.values + ] + fmt = "spreadsheet" + except: + raise ValueError("Format not recognized for file " + data_file.name) + if not isinstance(records, list): + records = [records] + return records, fmt + + +def record_to_formated_string(record, fmt="genbank", remove_descr=False): + if remove_descr: + record = deepcopy(record) + if isinstance(record, (list, tuple)): + for r in record: + r.description = "" + else: + record.description = "" + fileobject = StringIO() + write_record(record, fileobject, fmt) + return fileobject.getvalue().encode("utf-8") + + +def records_from_data_files(data_files, use_file_names_as_ids=False): + records = [] + for file_ in data_files: + circular = ("circular" not in file_) or file_.circular + if file_.name.lower().endswith("zip"): + records += records_from_zip_file( + file_, use_file_names_as_ids=use_file_names_as_ids + ) + continue + recs, fmt = records_from_data_file(file_) + single_record = len(recs) == 1 + for i, record in enumerate(recs): + record.circular = circular + record.linear = not circular + name_no_extension = "".join(file_.name.split(".")[:-1]) + name = name_no_extension + ("" if single_record else ("%04d" % i)) + name = name.replace(" ", "_") + UNKNOWN_IDS = [ + "None", + "", + "", + ".", + "EXPORTED", + "", + "Exported", + ] + # Sorry for this parts, it took a lot of "whatever works". + # keep your part names under 20c and pointless, and everything + # will be good + if str(record.id).strip() in UNKNOWN_IDS: + record.id = name + if str(record.name).strip() in UNKNOWN_IDS: + record.name = name + record.file_name = name_no_extension + if use_file_names_as_ids and single_record: + basename = os.path.basename(record.source_file) + basename_no_extension = os.path.splitext(basename)[0] + record.id = basename_no_extension + records += recs + return records + + +def data_to_html_data(data, datatype, filename=None): + """Data types: zip, genbank, fasta, pdf""" + datatype = { + "zip": "application/zip", + "genbank": "application/genbank", + "fasta": "application/fasta", + "pdf": "application/pdf", + "xlsx": "application/vnd.openxmlformats-officedocument.spreadsheetml.sheet", + }.get(datatype, datatype) + datatype = "data:%s;" % datatype + data64 = "base64,%s" % b64encode(data).decode("utf-8") + headers = "" + if filename is not None: + headers += "headers=filename%3D" + filename + ";" + return datatype + headers + data64 + + +def zip_data_to_html_data(data): + return data_to_html_data(data, "application/zip") + + +LADDERS = {"100_to_4k": bw.ladders.LADDER_100_to_4k} + + +def matplotlib_figure_to_svg_base64_data(fig, **kwargs): + """Return a string of the form 'data:image/svg+xml;base64,XXX' where XXX + is the base64-encoded svg version of the figure.""" + output = BytesIO() + fig.savefig(output, format="svg", **kwargs) + svg_txt = output.getvalue().decode("utf-8") + svg_txt = "\n".join(svg_txt.split("\n")[4:]) + svg_txt = "".join(svg_txt.split("\n")) + + content = b64encode(svg_txt.encode("utf-8")) + result = (b"data:image/svg+xml;base64," + content).decode("utf-8") + + return result + + +def matplotlib_figure_to_bitmap_base64_data(fig, fmt="png", **kwargs): + """Return a string of the form 'data:image/png;base64,XXX' where XXX + is the base64-encoded svg version of the figure.""" + output = BytesIO() + fig.savefig(output, format=fmt, **kwargs) + bitmap = output.getvalue() + content = b64encode(bitmap) + result = (b"data:image/%s;base64,%s" % (fmt.encode("utf-8"), content)).decode( + "utf-8" + ) + return result + + +def figures_to_pdf_report_data(figures, filename="report.pdf"): + pdf_io = BytesIO() + with PdfPages(pdf_io) as pdf: + for fig in figures: + pdf.savefig(fig, bbox_inches="tight") + return { + "data": ( + "data:application/pdf;base64," + + b64encode(pdf_io.getvalue()).decode("utf-8") + ), + "name": filename, + "mimetype": "application/pdf", + } + + +def csv_to_list(csv_string, sep=","): + return [ + element.strip() + for line in csv_string.split("\n") + for element in line.split(sep) + if len(element.strip()) + ] + + +def set_record_topology(record, topology): + """Set the Biopython record's topology, possibly passing if already set. + + This actually sets the ``record.annotations['topology']``.The ``topology`` + parameter can be "circular", "linear", "default_to_circular" (will default + to circular if ``annotations['topology']`` is not already set) or + "default_to_linear". + """ + valid_topologies = [ + "circular", + "linear", + "default_to_circular", + "default_to_linear", + ] + if topology not in valid_topologies: + raise ValueError( + "topology (%s) should be one of %s." + % (topology, ", ".join(valid_topologies)) + ) + annotations = record.annotations + default_prefix = "default_to_" + if topology.startswith(default_prefix): + if "topology" not in annotations: + annotations["topology"] = topology[len(default_prefix) :] + else: + annotations["topology"] = topology + + +############################################################################## +def main(): + + parser = argparse.ArgumentParser(description="Generate picklist for DNA assembly.") + parser.add_argument("--parts_files", help="Directory with parts data or file with part sizes") + parser.add_argument("--picklist", type=str, help="Path to the assembly plan CSV or Excel file") + parser.add_argument("--source_plate", help="Source plate file (CSV or Excel)") + parser.add_argument("--backbone_name", help="Name of the backbone") + parser.add_argument("--result_zip", help="Name of the output zip file") + parser.add_argument("--part_backbone_ratio", type=float, help="Part to backbone molar ratio") + parser.add_argument("--quantity_unit", choices=["fmol", "nM", "ng"], help="Quantity unit") + parser.add_argument("--part_quantity", type=float, help="Quantity of each part") + parser.add_argument("--buffer_volume", type=float, help="Buffer volume in µL") + parser.add_argument("--total_volume", type=float, help="Total reaction volume in µL") + parser.add_argument("--dispenser", choices=["labcyte_echo", "tecan_evo"], help="Dispenser machine") + + args = parser.parse_args() + + # Parameters: + picklist = args.picklist # assembly plan + # directory or can be a csv/Excel with part sizes + if isinstance(args.parts_files, str): + args.parts_files = args.parts_files.split(",") + parts_dir = fix_and_rename_paths(args.parts_files) + source_plate_path = args.source_plate + backbone_name = args.backbone_name + part_backbone_ratio = args.part_backbone_ratio + result_zip_file = args.result_zip # output file name "picklist.zip" + ############################################################################## + # Defaults: + destination_plate = None + destination_type = "new" # this parameter is not actually used + destination_size = 96 # this parameter is not actually used + fill_by = "column" # this parameter is not actually used + quantity_unit = args.quantity_unit + part_quantity = args.part_quantity # 1.3 + buffer_volume = args.buffer_volume # 0.3 # (µL) + total_volume = args.total_volume # 1 # (µL) + dispenser_machine = args.dispenser + dispenser_min_volume = 0.5 # (nL), this parameter is not actually used + dispenser_max_volume = 5 # (µL), this parameter is not actually used + dispenser_resolution = 2.5 # (nL), this parameter is not actually used + dispenser_dead_volume = 8 # (µL), this parameter is not actually used + use_file_names_as_ids = True + + # CODE + if picklist.endswith(".csv"): + csv = picklist.read().decode() + rows = [line.split(",") for line in csv.split("\n") if len(line)] + else: + dataframe = pandas.read_excel(picklist) + rows = [row for i, row in dataframe.iterrows()] + + assembly_plan = AssemblyPlan( + OrderedDict( + [ + ( + row[0], + [ + str(e).strip() + for e in row[1:] + if str(e).strip() not in ["-", "nan", ""] + ], + ) + for row in rows + if row[0] not in ["nan", "Construct name", "constructs", "construct"] + ] + ) + ) + for assembly, parts in assembly_plan.assemblies.items(): + assembly_plan.assemblies[assembly] = [part.replace(" ", "_") for part in parts] + + # Reading part infos + if not isinstance(parts_dir, list): + if parts_dir.endswith((".csv", ".xls", ".xlsx")): # part sizes specified in table + if parts_dir.endswith(".csv"): + dataframe = pandas.read_csv(parts_dir) + else: + dataframe = pandas.read_excel(parts_dir) + parts_data = {row.part: {"size": row["size"]} for i, row in dataframe.iterrows()} + else: # input records + records = dnacauldron.biotools.load_records_from_files( + files=parts_dir, use_file_names_as_ids=use_file_names_as_ids + ) + parts_data = {rec.id.replace(" ", "_").lower(): {"record": rec} for rec in records} + #parts_data = process_parts_with_mapping(records, args.file_name_mapping) + assembly_plan.parts_data = parts_data + parts_without_data = assembly_plan.parts_without_data() + if len(parts_without_data): + print("success: False") + print("message: Some parts have no provided record or data.") + print("missing_parts: ", parts_without_data) + sys.exit() + # Reading protocol + if quantity_unit == "fmol": + part_mol = part_quantity * 1e-15 + part_g = None + if quantity_unit == "nM": + part_mol = part_quantity * total_volume * 1e-15 + part_g = None + if quantity_unit == "ng": + part_mol = None + part_g = part_quantity * 1e-9 + # Backbone:part molar ratio calculation is not performed in this case. + # This ensures no change regardless of form input: + part_backbone_ratio = 1 + print("Generating picklist") + picklist_generator = AssemblyPicklistGenerator( + part_mol=part_mol, + part_g=part_g, + complement_to=total_volume * 1e-6, # convert uL to L + buffer_volume=buffer_volume * 1e-6, + volume_rounding=2.5e-9, # not using parameter from form + minimal_dispense_volume=5e-9, # Echo machine's minimum dispense - + ) + backbone_name_list = backbone_name.split(",") + source_plate = plate_from_content_spreadsheet(source_plate_path) + + for well in source_plate.iter_wells(): + if well.is_empty: + continue + quantities = well.content.quantities + part, quantity = list(quantities.items())[0] + quantities.pop(part) + quantities[part.replace(" ", "_")] = quantity + + if part in backbone_name_list: + # This section multiplies the backbone concentration with the + # part:backbone molar ratio. This tricks the calculator into making + # a picklist with the desired ratio. + # For example, a part:backbone = 2:1 will multiply the + # backbone concentration by 2, therefore half as much of it will be + # added to the well. + quantities[part.replace(" ", "_")] = quantity * part_backbone_ratio + else: + quantities[part.replace(" ", "_")] = quantity + + source_plate.name = "Source" + if destination_plate: + dest_filelike = file_to_filelike_object(destination_plate) + destination_plate = plate_from_content_spreadsheet(destination_plate) + else: + destination_plate = Plate4ti0960("Mixplate") + destination_wells = ( + well for well in destination_plate.iter_wells(direction="column") if well.is_empty + ) + picklist, picklist_data = picklist_generator.make_picklist( + assembly_plan, + source_wells=source_plate.iter_wells(), + destination_wells=destination_wells, + ) + if picklist is None: + print("success: False") + print("message: Some parts in the assembly plan have no corresponding well.") + print("picklist_data: ", picklist_data) + print("missing_parts:", picklist_data.get("missing_parts", None)) + sys.exit() + + future_plates = picklist.simulate(inplace=False) + + + def text(w): + txt = human_volume(w.content.volume) + if "construct" in w.data: + txt = "\n".join([w.data["construct"], txt]) + return txt + + + plotter = PlateTextPlotter(text) + ax, _ = plotter.plot_plate(future_plates[destination_plate], figsize=(20, 8)) + + ziproot = flametree.file_tree(result_zip_file, replace=True) + + # MIXPLATE MAP PLOT + ax.figure.savefig( + ziproot._file("final_mixplate.pdf").open("wb"), + format="pdf", + bbox_inches="tight", + ) + plt.close(ax.figure) + plate_to_platemap_spreadsheet( + future_plates[destination_plate], + lambda w: w.data.get("construct", ""), + filepath=ziproot._file("final_mixplate.xls").open("wb"), + ) + + # ASSEMBLY REPORT + print("Writing report...") + picklist_to_assembly_mix_report( + picklist, + ziproot._file("assembly_mix_picklist_report.pdf").open("wb"), + data=picklist_data, + ) + assembly_plan.write_report(ziproot._file("assembly_plan_summary.pdf").open("wb")) + + # MACHINE PICKLIST + + if dispenser_machine == "labcyte_echo": + picklist_to_labcyte_echo_picklist_file( + picklist, ziproot._file("ECHO_picklist.csv").open("w") + ) + else: + picklist_to_tecan_evo_picklist_file( + picklist, ziproot._file("EVO_picklist.gwl").open("w") + ) + # We'll not write the input source plate. + # raw = file_to_filelike_object(source_plate_path).read() + # f = ziproot.copy(source_plate_path) + # f.write(raw, mode="wb") + ziproot._close() + print("success: True") + + +if __name__ == "__main__": + main() diff --git a/tools/create_assembly_picklists/create_assembly_picklists.xml b/tools/create_assembly_picklists/create_assembly_picklists.xml new file mode 100644 index 00000000..b06324b7 --- /dev/null +++ b/tools/create_assembly_picklists/create_assembly_picklists.xml @@ -0,0 +1,206 @@ + + Provide a source plate map and an assembly plan, get a robotic picklist spreadsheet for Tecan EVO or Labcyte Echo + + 0 + 0.1.0 + + + fuzzywuzzy + bandwagon + biopython + crazydoc + dnacauldron + dnachisel + flametree + plateo + snapgene-reader + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + `_ + + ]]> + + + @unpublished{create_assembly_picklists + author = {Ramiz Khaled}, + title = {{create_assembly_picklists}}, + url = {https://github.com/Edinburgh-Genome-Foundry/CUBA/blob/master/backend/app/views/create_assembly_picklists/CreateAssemblyPicklistsView.py}, + } + + + diff --git a/tools/create_assembly_picklists/test-data/emma_parts/HC_Amp_ccdB.gb b/tools/create_assembly_picklists/test-data/emma_parts/HC_Amp_ccdB.gb new file mode 100644 index 00000000..77cd26fa --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/HC_Amp_ccdB.gb @@ -0,0 +1,109 @@ +LOCUS Exported 2721 bp ds-DNA circular SYN 14-SEP-2017 +DEFINITION synthetic circular DNA. +ACCESSION . +VERSION . +KEYWORDS HC_Amp_ccdB(1-25).gb +SOURCE synthetic DNA construct + ORGANISM synthetic DNA construct +REFERENCE 1 (bases 1 to 2721) + AUTHORS Trial User + TITLE Direct Submission + JOURNAL Exported Sep 14, 2017 from SnapGene Viewer 4.0.2 + http://www.snapgene.com +FEATURES Location/Qualifiers + source 1..2721 + /organism="synthetic DNA construct" + /mol_type="other DNA" + misc_feature complement(73..78) + /label=BsmBI + misc_feature 129..462 + /label=*ccdB promoter* + exon 463..768 + /label=ccdB + /note="ccdB" + terminator 809..880 + /note="rrnB T1 terminator + transcription terminator T1 from the E. coli rrnB gene" + terminator 896..923 + /note="T7Te terminator + phage T7 early transcription terminator" + misc_feature 930..942 + /label=BioBrick suffix + /note="universal suffix for all parts" + misc_feature 943..948 + /label=BsmBI + terminator 1027..1056 + /note="T3Te terminator + phage T3 early transcription terminator" + rep_origin 1078..1665 + /direction=RIGHT + /label=ori + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1677..1704 + /note="T7Te terminator + phage T7 early transcription terminator" + CDS complement(1728..2588) + /codon_start=1 + /gene="bla" + /product="beta-lactamase" + /note="AmpR + confers resistance to ampicillin, carbenicillin, and + related antibiotics" + /translation="MSIQHFRVALIPFFAAFCLPVFAHPETLVKVKDAEDQLGARVGYI + ELDLNSGKILESLRPEERFPMMSTFKVLLCGAVLSRIDAGQEQLGRRIHYSQNDLVEYS + PVTEKHLTDGMTVRELCSAAITMSDNTAANLLLATIGGPKELTAFLHNMGDHVTRLDRW + EPELNEAIPNDERDTTMPVAMATTLRKLLTGELLTLASRQQLIDWMEADKVAGSLLRSA + LPAGWFIADKSGAGERGSRGIIAALGPDGKPSRIVVIYTTGSQATMDERNRQIAEIGAS + LIKHW" + promoter complement(2589..2691) + /note="cat promoter + promoter of the E. coli cat gene" +ORIGIN + 1 ctttctgcta tggaggtcag gtatgattta aatggtcagt attgagcgat atctagagaa + 61 ttcgtcatag gagagacgca atacgcaaac cgcctctccc cgcgcgttgg ccgattcatt + 121 aatgcaggga tccggcttac taaaagccag ataacagtat gcgtatttgc gcgctgattt + 181 ttgcggtata agaatatata ctgatatgta tacccgaagt atgtcaaaaa gaggtatgct + 241 atgaagcagc gtattacagt gacagttgac agcgacagct atcagttgct caaggcatat + 301 atgatgtcaa tatctccggt ctggtaagca caaccatgca gaatgaagcc cgtcgtctgc + 361 gtgccgaacg ctggaaagcg gaaaatcagg aagggatggc tgaggtcgcc cggtttattg + 421 aaatgaacgg ctcttttgct gacgagaaca ggggctggtg aaatgcagtt taaggtttac + 481 acctataaaa gagagagccg ttatcgtctg tttgtggatg tacagagtga tattattgac + 541 acgcccgggc gacggatggt gatccccctg gccagtgcac gtctgctgtc agataaagtc + 601 ccccgtgaac tttacccggt ggtgcatatc ggggatgaaa gctggcgcat gatgaccacc + 661 gatatggcca gtgtgccggt ctccgttatc ggggaagaag tggctgatct cagccaccgc + 721 gaaaatgaca tcaaaaacgc cattaacctg atgttctggg gaatataagc tgatagtgct + 781 agtgtagatc gctactagag ccaggcatca aataaaacga aaggctcagt cgaaagactg + 841 ggcctttcgt tttatctgtt gtttgtcggt gaacgctctc tactagagtc acactggctc + 901 accttcgggt gggcctttct gcgtttatat actagtagcg gccgtctcaa cgataacgaa + 961 ttcaagcttg atatcattca ggacgagcct cagactccag cgtaactgga ctgcaatcaa + 1021 ctcactggct caccttcacg ggtgggcctt tcttcggtag aaaatcaaag gatcttcttg + 1081 agatcctttt tttctgcgcg taatctgctg cttgcaaaca aaaaaaccac cgctaccagc + 1141 ggtggtttgt ttgccggatc aagagctacc aactcttttt ccgaggtaac tggcttcagc + 1201 agagcgcaga taccaaatac tgttcttcta gtgtagccgt agttaggcca ccacttcaag + 1261 aactctgtag caccgcctac atacctcgct ctgctaatcc tgttaccagt ggctgctgcc + 1321 agtggcgata agtcgtgtct taccgggttg gactcaagac gatagttacc ggataaggcg + 1381 cagcggtcgg gctgaacggg gggttcgtgc acacagccca gcttggagcg aacgacctac + 1441 accgaactga gatacctaca gcgtgagcta tgagaaagcg ccacgcttcc cgaagggaga + 1501 aaggcggaca ggtatccggt aagcggcagg gtcggaacag gagagcgcac gagggagctt + 1561 ccagggggaa acgcctggta tctttatagt cctgtcgggt ttcgccacct ctgacttgag + 1621 catcgatttt tgtgatgctc gtcagggggg cggagcctat ggaaaaacgc cagcaacgca + 1681 gaaaggccca cccgaaggtg agccaggtga ttacatttgg gccctcatta ccaatgctta + 1741 atcagtgagg cacctatctc agcgatctgt ctatttcgtt catccatagt tgcctgactc + 1801 cccgtcgtgt agataactac gatgcgggag ggcttaccat ctggccccag tgctgcaatg + 1861 ataccgcgag aaccacgctc accggctcca gatttatcag caataaacca gccagccggg + 1921 agggccgagc gcagaagtga tcctgcaact ttatccgcct ccatccagtc tattaattgt + 1981 tgccgggaag ctagagtaag tagttcgcca gttaatagtt tgcgcaacgt tgttgccatt + 2041 gctacaggca tcgtggtgtc acgctcgtcg tttggtatgg cttcattcag ctccggttcc + 2101 caacgatcaa ggcgagttac atgatccccc atgttgtgca aaaaagcggt tagctccttc + 2161 ggtcctccga tcgttgccag aagtaagttg gccgcagtgt tatcactcat ggttatggca + 2221 gcactgcata attctcttac tgtcatgcca tccgtgagat gcttttctgt gactggtgag + 2281 tactcaacca agtcattctg agaatagtgt atgcggcgac cgagttgctc ttgcccggcg + 2341 tcaatacggg ataataccgc gccacatagc agaactttaa aagtgctcat cattggaaaa + 2401 cgttcttcgg ggcgtaaact ctcaaggatc ttaccgctgt tgagatccag ttcgatgtaa + 2461 cccactcgtg cacccaactg atcttcagca tcttttactt tcaccagcgt ttctgggtga + 2521 gcaaaaacag gaaggcaaaa tgccgcaaaa aagggaataa gggcgacacg gaaatgttga + 2581 atactcattt tagcttcctt agctcctgaa aatctcgata actcaaaaaa tacgcccggt + 2641 agtgatctta tttcattatg gtgaaagttg gaacctctta cgtgccgatc aagtcaaaag + 2701 cctccggtcg gaggcttttg a +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/conn a-c.gb b/tools/create_assembly_picklists/test-data/emma_parts/conn a-c.gb new file mode 100644 index 00000000..620e10c0 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/conn a-c.gb @@ -0,0 +1,76 @@ +LOCUS . 1905 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /note="From Exported" + /source="Exported" + misc_feature complement(1154..1245) + /note="conn A-C" + source complement(1154..1245) + /note="From Exported" + /source="Exported" + misc_feature complement(1251..1256) + /note="BsmBI" + terminator 1323..1354 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1355..1457 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1250..1905 + /note="From Exported" + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcga gtccagatag acaggaagaa tcgacagaac atccgacgaa tagaggacca + 1201 cgggcagcag aagaccatgt ctaaagtgcg agactgaata caagacctac gagacgaaga + 1261 cgaattctct agatatcgct caatactgac catttaaatc atacctgacc tccatagcag + 1321 aaagtcaaaa gcctccgacc ggaggctttt gacttgatcg gcacgtaaga ggttccaact + 1381 ttcaccataa tgaaataaga tcactaccgg gcgtattttt tgagttatcg agattttcag + 1441 gagctaagga agctaaaatg agccatattc aacgggaaac gtcttgctcg aggccgcgat + 1501 taaattccaa catggatgct gatttatatg ggtataaatg ggctcgcgat aatgtcgggc + 1561 aatcaggtgc gacaatctat cgattgtatg ggaagcccga tgcgccagag ttgtttctga + 1621 aacatggcaa aggtagcgtt gccaatgatg ttacagatga gatggtcagg ctaaactggc + 1681 tgacggaatt tatgcctctt ccgaccatca agcattttat ccgtactcct gatgatgcat + 1741 ggttactcac cactgcgatc ccagggaaaa cagcattcca ggtattagaa gaatatcctg + 1801 attcaggtga aaatattgtt gatgcgctgg cagtgttcct gcgccggttg cattcgattc + 1861 ctgtttgtaa ttgtcctttt aacggcgatc gcgtatttcg tctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/conn b-e.gb b/tools/create_assembly_picklists/test-data/emma_parts/conn b-e.gb new file mode 100644 index 00000000..d4212a12 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/conn b-e.gb @@ -0,0 +1,75 @@ +LOCUS . 1853 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /note="From Exported" + /source="Exported" + misc_feature complement(1154..1193) + /note="conn B-E" + source complement(1154..1193) + /note="From Exported" + /source="Exported" + misc_feature complement(1199..1204) + /note="BsmBI" + terminator 1271..1302 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1303..1405 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1198..1853 + /note="From Exported" + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc ggatctctca atctccttct aagtctcttt caccgtagtt agtccatcga + 1201 gacgaagacg aattctctag atatcgctca atactgacca tttaaatcat acctgacctc + 1261 catagcagaa agtcaaaagc ctccgaccgg aggcttttga cttgatcggc acgtaagagg + 1321 ttccaacttt caccataatg aaataagatc actaccgggc gtattttttg agttatcgag + 1381 attttcagga gctaaggaag ctaaaatgag ccatattcaa cgggaaacgt cttgctcgag + 1441 gccgcgatta aattccaaca tggatgctga tttatatggg tataaatggg ctcgcgataa + 1501 tgtcgggcaa tcaggtgcga caatctatcg attgtatggg aagcccgatg cgccagagtt + 1561 gtttctgaaa catggcaaag gtagcgttgc caatgatgtt acagatgaga tggtcaggct + 1621 aaactggctg acggaattta tgcctcttcc gaccatcaag cattttatcc gtactcctga + 1681 tgatgcatgg ttactcacca ctgcgatccc agggaaaaca gcattccagg tattagaaga + 1741 atatcctgat tcaggtgaaa atattgttga tgcgctggca gtgttcctgc gccggttgca + 1801 ttcgattcct gtttgtaatt gtccttttaa cggcgatcgc gtatttcgtc tcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/conn b-l.gb b/tools/create_assembly_picklists/test-data/emma_parts/conn b-l.gb new file mode 100644 index 00000000..b5ba2525 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/conn b-l.gb @@ -0,0 +1,75 @@ +LOCUS . 1853 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /note="From Exported" + /source="Exported" + misc_feature complement(1154..1193) + /note="conn B-L" + source complement(1154..1193) + /note="From Exported" + /source="Exported" + misc_feature complement(1199..1204) + /note="BsmBI" + terminator 1271..1302 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1303..1405 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1198..1853 + /note="From Exported" + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgg acgtaaatgg gaggcaggta agtggagatt ccaagcgacc agtccatcga + 1201 gacgaagacg aattctctag atatcgctca atactgacca tttaaatcat acctgacctc + 1261 catagcagaa agtcaaaagc ctccgaccgg aggcttttga cttgatcggc acgtaagagg + 1321 ttccaacttt caccataatg aaataagatc actaccgggc gtattttttg agttatcgag + 1381 attttcagga gctaaggaag ctaaaatgag ccatattcaa cgggaaacgt cttgctcgag + 1441 gccgcgatta aattccaaca tggatgctga tttatatggg tataaatggg ctcgcgataa + 1501 tgtcgggcaa tcaggtgcga caatctatcg attgtatggg aagcccgatg cgccagagtt + 1561 gtttctgaaa catggcaaag gtagcgttgc caatgatgtt acagatgaga tggtcaggct + 1621 aaactggctg acggaattta tgcctcttcc gaccatcaag cattttatcc gtactcctga + 1681 tgatgcatgg ttactcacca ctgcgatccc agggaaaaca gcattccagg tattagaaga + 1741 atatcctgat tcaggtgaaa atattgttga tgcgctggca gtgttcctgc gccggttgca + 1801 ttcgattcct gtttgtaatt gtccttttaa cggcgatcgc gtatttcgtc tcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/conn d-e.gb b/tools/create_assembly_picklists/test-data/emma_parts/conn d-e.gb new file mode 100644 index 00000000..54af4d85 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/conn d-e.gb @@ -0,0 +1,75 @@ +LOCUS . 1855 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /note="From Exported" + /source="Exported" + misc_feature complement(1154..1195) + /note="conn D-E" + source complement(1154..1195) + /note="From Exported" + /source="Exported" + misc_feature complement(1201..1206) + /note="BsmBI" + terminator 1273..1304 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1305..1407 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1200..1855 + /note="From Exported" + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc ggatagatcg atctgaatta attctgacgg ttcactaaag gctaagtccc + 1201 gagacgaaga cgaattctct agatatcgct caatactgac catttaaatc atacctgacc + 1261 tccatagcag aaagtcaaaa gcctccgacc ggaggctttt gacttgatcg gcacgtaaga + 1321 ggttccaact ttcaccataa tgaaataaga tcactaccgg gcgtattttt tgagttatcg + 1381 agattttcag gagctaagga agctaaaatg agccatattc aacgggaaac gtcttgctcg + 1441 aggccgcgat taaattccaa catggatgct gatttatatg ggtataaatg ggctcgcgat + 1501 aatgtcgggc aatcaggtgc gacaatctat cgattgtatg ggaagcccga tgcgccagag + 1561 ttgtttctga aacatggcaa aggtagcgtt gccaatgatg ttacagatga gatggtcagg + 1621 ctaaactggc tgacggaatt tatgcctctt ccgaccatca agcattttat ccgtactcct + 1681 gatgatgcat ggttactcac cactgcgatc ccagggaaaa cagcattcca ggtattagaa + 1741 gaatatcctg attcaggtga aaatattgtt gatgcgctgg cagtgttcct gcgccggttg + 1801 cattcgattc ctgtttgtaa ttgtcctttt aacggcgatc gcgtatttcg tctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/conn d-f.gb b/tools/create_assembly_picklists/test-data/emma_parts/conn d-f.gb new file mode 100644 index 00000000..743070e3 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/conn d-f.gb @@ -0,0 +1,75 @@ +LOCUS . 1855 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /note="From Exported" + /source="Exported" + misc_feature complement(1154..1195) + /note="conn D-F" + source complement(1154..1195) + /note="From Exported" + /source="Exported" + misc_feature complement(1201..1206) + /note="BsmBI" + terminator 1273..1304 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1305..1407 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1200..1855 + /note="From Exported" + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc tggtagatcg atctgaatta attctgacgg ttcactaaag gctaagtccc + 1201 gagacgaaga cgaattctct agatatcgct caatactgac catttaaatc atacctgacc + 1261 tccatagcag aaagtcaaaa gcctccgacc ggaggctttt gacttgatcg gcacgtaaga + 1321 ggttccaact ttcaccataa tgaaataaga tcactaccgg gcgtattttt tgagttatcg + 1381 agattttcag gagctaagga agctaaaatg agccatattc aacgggaaac gtcttgctcg + 1441 aggccgcgat taaattccaa catggatgct gatttatatg ggtataaatg ggctcgcgat + 1501 aatgtcgggc aatcaggtgc gacaatctat cgattgtatg ggaagcccga tgcgccagag + 1561 ttgtttctga aacatggcaa aggtagcgtt gccaatgatg ttacagatga gatggtcagg + 1621 ctaaactggc tgacggaatt tatgcctctt ccgaccatca agcattttat ccgtactcct + 1681 gatgatgcat ggttactcac cactgcgatc ccagggaaaa cagcattcca ggtattagaa + 1741 gaatatcctg attcaggtga aaatattgtt gatgcgctgg cagtgttcct gcgccggttg + 1801 cattcgattc ctgtttgtaa ttgtcctttt aacggcgatc gcgtatttcg tctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/conn h-ha.gb b/tools/create_assembly_picklists/test-data/emma_parts/conn h-ha.gb new file mode 100644 index 00000000..f7c24372 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/conn h-ha.gb @@ -0,0 +1,80 @@ +LOCUS . 1861 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /note="From Exported" + /source="Exported" + misc_feature complement(1154..1201) + /note="conn H-Ha" + source complement(1154..1201) + /note="From Exported" + /source="Exported" + CDS complement(1199..1201) + /codon_start=1 + /note="STOP" + /translation="" + misc_feature complement(1207..1212) + /note="BsmBI" + terminator 1279..1310 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1311..1413 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1206..1861 + /note="From Exported" + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgg gatcgaggat atcacctgta gggatgttct agagtccgga agctgttatt + 1201 agcctcgaga cgaagacgaa ttctctagat atcgctcaat actgaccatt taaatcatac + 1261 ctgacctcca tagcagaaag tcaaaagcct ccgaccggag gcttttgact tgatcggcac + 1321 gtaagaggtt ccaactttca ccataatgaa ataagatcac taccgggcgt attttttgag + 1381 ttatcgagat tttcaggagc taaggaagct aaaatgagcc atattcaacg ggaaacgtct + 1441 tgctcgaggc cgcgattaaa ttccaacatg gatgctgatt tatatgggta taaatgggct + 1501 cgcgataatg tcgggcaatc aggtgcgaca atctatcgat tgtatgggaa gcccgatgcg + 1561 ccagagttgt ttctgaaaca tggcaaaggt agcgttgcca atgatgttac agatgagatg + 1621 gtcaggctaa actggctgac ggaatttatg cctcttccga ccatcaagca ttttatccgt + 1681 actcctgatg atgcatggtt actcaccact gcgatcccag ggaaaacagc attccaggta + 1741 ttagaagaat atcctgattc aggtgaaaat attgttgatg cgctggcagt gttcctgcgc + 1801 cggttgcatt cgattcctgt ttgtaattgt ccttttaacg gcgatcgcgt atttcgtctc + 1861 g +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/conn h-j.gb b/tools/create_assembly_picklists/test-data/emma_parts/conn h-j.gb new file mode 100644 index 00000000..2479f8bd --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/conn h-j.gb @@ -0,0 +1,80 @@ +LOCUS . 1861 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /note="From Exported" + /source="Exported" + misc_feature complement(1154..1201) + /note="conn H-J" + source complement(1154..1201) + /note="From Exported" + /source="Exported" + CDS complement(1199..1201) + /codon_start=1 + /note="STOP" + /translation="" + misc_feature complement(1207..1212) + /note="BsmBI" + terminator 1279..1310 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1311..1413 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1206..1861 + /note="From Exported" + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcga gcacgaggat atcacctgta gggatgttct agagtccgga agctgttatt + 1201 agcctcgaga cgaagacgaa ttctctagat atcgctcaat actgaccatt taaatcatac + 1261 ctgacctcca tagcagaaag tcaaaagcct ccgaccggag gcttttgact tgatcggcac + 1321 gtaagaggtt ccaactttca ccataatgaa ataagatcac taccgggcgt attttttgag + 1381 ttatcgagat tttcaggagc taaggaagct aaaatgagcc atattcaacg ggaaacgtct + 1441 tgctcgaggc cgcgattaaa ttccaacatg gatgctgatt tatatgggta taaatgggct + 1501 cgcgataatg tcgggcaatc aggtgcgaca atctatcgat tgtatgggaa gcccgatgcg + 1561 ccagagttgt ttctgaaaca tggcaaaggt agcgttgcca atgatgttac agatgagatg + 1621 gtcaggctaa actggctgac ggaatttatg cctcttccga ccatcaagca ttttatccgt + 1681 actcctgatg atgcatggtt actcaccact gcgatcccag ggaaaacagc attccaggta + 1741 ttagaagaat atcctgattc aggtgaaaat attgttgatg cgctggcagt gttcctgcgc + 1801 cggttgcatt cgattcctgt ttgtaattgt ccttttaacg gcgatcgcgt atttcgtctc + 1861 g +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/conn h-k.gb b/tools/create_assembly_picklists/test-data/emma_parts/conn h-k.gb new file mode 100644 index 00000000..ece44db3 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/conn h-k.gb @@ -0,0 +1,80 @@ +LOCUS . 1861 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /note="From Exported" + /source="Exported" + misc_feature complement(1154..1201) + /note="conn H-K" + source complement(1154..1201) + /note="From Exported" + /source="Exported" + CDS complement(1199..1201) + /codon_start=1 + /note="STOP" + /translation="" + misc_feature complement(1207..1212) + /note="BsmBI" + terminator 1279..1310 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1311..1413 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1206..1861 + /note="From Exported" + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgt acccgaggat atcacctgta gggatgttct agagtccgga agctgttatt + 1201 agcctcgaga cgaagacgaa ttctctagat atcgctcaat actgaccatt taaatcatac + 1261 ctgacctcca tagcagaaag tcaaaagcct ccgaccggag gcttttgact tgatcggcac + 1321 gtaagaggtt ccaactttca ccataatgaa ataagatcac taccgggcgt attttttgag + 1381 ttatcgagat tttcaggagc taaggaagct aaaatgagcc atattcaacg ggaaacgtct + 1441 tgctcgaggc cgcgattaaa ttccaacatg gatgctgatt tatatgggta taaatgggct + 1501 cgcgataatg tcgggcaatc aggtgcgaca atctatcgat tgtatgggaa gcccgatgcg + 1561 ccagagttgt ttctgaaaca tggcaaaggt agcgttgcca atgatgttac agatgagatg + 1621 gtcaggctaa actggctgac ggaatttatg cctcttccga ccatcaagca ttttatccgt + 1681 actcctgatg atgcatggtt actcaccact gcgatcccag ggaaaacagc attccaggta + 1741 ttagaagaat atcctgattc aggtgaaaat attgttgatg cgctggcagt gttcctgcgc + 1801 cggttgcatt cgattcctgt ttgtaattgt ccttttaacg gcgatcgcgt atttcgtctc + 1861 g +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/conn j-k.gb b/tools/create_assembly_picklists/test-data/emma_parts/conn j-k.gb new file mode 100644 index 00000000..b63de708 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/conn j-k.gb @@ -0,0 +1,75 @@ +LOCUS . 1855 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /note="From Exported" + /source="Exported" + misc_feature complement(1154..1195) + /note="conn J-K" + source complement(1154..1195) + /note="From Exported" + /source="Exported" + misc_feature complement(1201..1206) + /note="BsmBI" + terminator 1273..1304 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1305..1407 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1200..1855 + /note="From Exported" + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgt accgttcctt cctgtattgt ctccttccgt gtttcagtta gcctcagcac + 1201 gagacgaaga cgaattctct agatatcgct caatactgac catttaaatc atacctgacc + 1261 tccatagcag aaagtcaaaa gcctccgacc ggaggctttt gacttgatcg gcacgtaaga + 1321 ggttccaact ttcaccataa tgaaataaga tcactaccgg gcgtattttt tgagttatcg + 1381 agattttcag gagctaagga agctaaaatg agccatattc aacgggaaac gtcttgctcg + 1441 aggccgcgat taaattccaa catggatgct gatttatatg ggtataaatg ggctcgcgat + 1501 aatgtcgggc aatcaggtgc gacaatctat cgattgtatg ggaagcccga tgcgccagag + 1561 ttgtttctga aacatggcaa aggtagcgtt gccaatgatg ttacagatga gatggtcagg + 1621 ctaaactggc tgacggaatt tatgcctctt ccgaccatca agcattttat ccgtactcct + 1681 gatgatgcat ggttactcac cactgcgatc ccagggaaaa cagcattcca ggtattagaa + 1741 gaatatcctg attcaggtga aaatattgtt gatgcgctgg cagtgttcct gcgccggttg + 1801 cattcgattc ctgtttgtaa ttgtcctttt aacggcgatc gcgtatttcg tctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/conn l-n.gb b/tools/create_assembly_picklists/test-data/emma_parts/conn l-n.gb new file mode 100644 index 00000000..11480aa3 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/conn l-n.gb @@ -0,0 +1,76 @@ +LOCUS . 1905 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /note="From Exported" + /source="Exported" + misc_feature complement(1154..1245) + /note="conn L-N" + source complement(1154..1245) + /note="From Exported" + /source="Exported" + misc_feature complement(1251..1256) + /note="BsmBI" + terminator 1323..1354 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1355..1457 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1250..1905 + /note="From Exported" + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgg tagcctcctc ctatcctcat cacttcaacc ggatctactc tacaaccttc + 1201 cctatccact tcctccacat gctctccacc aacatcctca tcatagacgc gagacgaaga + 1261 cgaattctct agatatcgct caatactgac catttaaatc atacctgacc tccatagcag + 1321 aaagtcaaaa gcctccgacc ggaggctttt gacttgatcg gcacgtaaga ggttccaact + 1381 ttcaccataa tgaaataaga tcactaccgg gcgtattttt tgagttatcg agattttcag + 1441 gagctaagga agctaaaatg agccatattc aacgggaaac gtcttgctcg aggccgcgat + 1501 taaattccaa catggatgct gatttatatg ggtataaatg ggctcgcgat aatgtcgggc + 1561 aatcaggtgc gacaatctat cgattgtatg ggaagcccga tgcgccagag ttgtttctga + 1621 aacatggcaa aggtagcgtt gccaatgatg ttacagatga gatggtcagg ctaaactggc + 1681 tgacggaatt tatgcctctt ccgaccatca agcattttat ccgtactcct gatgatgcat + 1741 ggttactcac cactgcgatc ccagggaaaa cagcattcca ggtattagaa gaatatcctg + 1801 attcaggtga aaatattgtt gatgcgctgg cagtgttcct gcgccggttg cattcgattc + 1861 ctgtttgtaa ttgtcctttt aacggcgatc gcgtatttcg tctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/conn l-r.gb b/tools/create_assembly_picklists/test-data/emma_parts/conn l-r.gb new file mode 100644 index 00000000..ab485985 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/conn l-r.gb @@ -0,0 +1,76 @@ +LOCUS . 1905 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /note="From Exported" + /source="Exported" + misc_feature complement(1154..1245) + /note="conn L-R" + source complement(1154..1245) + /note="From Exported" + /source="Exported" + misc_feature complement(1251..1256) + /note="BsmBI" + terminator 1323..1354 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1355..1457 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1250..1905 + /note="From Exported" + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcga ccgcctcctc ctatcctcat cacttcaacc ggatctactc tacaaccttc + 1201 cctatccact tcctccacat gctctccacc aacatcctca tcatagacgc gagacgaaga + 1261 cgaattctct agatatcgct caatactgac catttaaatc atacctgacc tccatagcag + 1321 aaagtcaaaa gcctccgacc ggaggctttt gacttgatcg gcacgtaaga ggttccaact + 1381 ttcaccataa tgaaataaga tcactaccgg gcgtattttt tgagttatcg agattttcag + 1441 gagctaagga agctaaaatg agccatattc aacgggaaac gtcttgctcg aggccgcgat + 1501 taaattccaa catggatgct gatttatatg ggtataaatg ggctcgcgat aatgtcgggc + 1561 aatcaggtgc gacaatctat cgattgtatg ggaagcccga tgcgccagag ttgtttctga + 1621 aacatggcaa aggtagcgtt gccaatgatg ttacagatga gatggtcagg ctaaactggc + 1681 tgacggaatt tatgcctctt ccgaccatca agcattttat ccgtactcct gatgatgcat + 1741 ggttactcac cactgcgatc ccagggaaaa cagcattcca ggtattagaa gaatatcctg + 1801 attcaggtga aaatattgtt gatgcgctgg cagtgttcct gcgccggttg cattcgattc + 1861 ctgtttgtaa ttgtcctttt aacggcgatc gcgtatttcg tctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/conn l-w.gb b/tools/create_assembly_picklists/test-data/emma_parts/conn l-w.gb new file mode 100644 index 00000000..42d168b6 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/conn l-w.gb @@ -0,0 +1,76 @@ +LOCUS . 1905 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /note="From Exported" + /source="Exported" + misc_feature complement(1154..1245) + /note="conn L-W" + source complement(1154..1245) + /note="From Exported" + /source="Exported" + misc_feature complement(1251..1256) + /note="BsmBI" + terminator 1323..1354 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1355..1457 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1250..1905 + /note="From Exported" + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgt tcgcctcctc ctatcctcat cacttcaacc ggatctactc tacaaccttc + 1201 cctatccact tcctccacat gctctccacc aacatcctca tcatagacgc gagacgaaga + 1261 cgaattctct agatatcgct caatactgac catttaaatc atacctgacc tccatagcag + 1321 aaagtcaaaa gcctccgacc ggaggctttt gacttgatcg gcacgtaaga ggttccaact + 1381 ttcaccataa tgaaataaga tcactaccgg gcgtattttt tgagttatcg agattttcag + 1441 gagctaagga agctaaaatg agccatattc aacgggaaac gtcttgctcg aggccgcgat + 1501 taaattccaa catggatgct gatttatatg ggtataaatg ggctcgcgat aatgtcgggc + 1561 aatcaggtgc gacaatctat cgattgtatg ggaagcccga tgcgccagag ttgtttctga + 1621 aacatggcaa aggtagcgtt gccaatgatg ttacagatga gatggtcagg ctaaactggc + 1681 tgacggaatt tatgcctctt ccgaccatca agcattttat ccgtactcct gatgatgcat + 1741 ggttactcac cactgcgatc ccagggaaaa cagcattcca ggtattagaa gaatatcctg + 1801 attcaggtga aaatattgtt gatgcgctgg cagtgttcct gcgccggttg cattcgattc + 1861 ctgtttgtaa ttgtcctttt aacggcgatc gcgtatttcg tctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/conn l-y.gb b/tools/create_assembly_picklists/test-data/emma_parts/conn l-y.gb new file mode 100644 index 00000000..694aa79d --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/conn l-y.gb @@ -0,0 +1,76 @@ +LOCUS . 1905 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /note="From Exported" + /source="Exported" + misc_feature complement(1154..1245) + /note="conn L-Y" + source complement(1154..1245) + /note="From Exported" + /source="Exported" + misc_feature complement(1251..1256) + /note="BsmBI" + terminator 1323..1354 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1355..1457 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1250..1905 + /note="From Exported" + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc agtcctcctc ctatcctcat cacttcaacc ggatctactc tacaaccttc + 1201 cctatccact tcctccacat gctctccacc aacatcctca tcatagacgc gagacgaaga + 1261 cgaattctct agatatcgct caatactgac catttaaatc atacctgacc tccatagcag + 1321 aaagtcaaaa gcctccgacc ggaggctttt gacttgatcg gcacgtaaga ggttccaact + 1381 ttcaccataa tgaaataaga tcactaccgg gcgtattttt tgagttatcg agattttcag + 1441 gagctaagga agctaaaatg agccatattc aacgggaaac gtcttgctcg aggccgcgat + 1501 taaattccaa catggatgct gatttatatg ggtataaatg ggctcgcgat aatgtcgggc + 1561 aatcaggtgc gacaatctat cgattgtatg ggaagcccga tgcgccagag ttgtttctga + 1621 aacatggcaa aggtagcgtt gccaatgatg ttacagatga gatggtcagg ctaaactggc + 1681 tgacggaatt tatgcctctt ccgaccatca agcattttat ccgtactcct gatgatgcat + 1741 ggttactcac cactgcgatc ccagggaaaa cagcattcca ggtattagaa gaatatcctg + 1801 attcaggtga aaatattgtt gatgcgctgg cagtgttcct gcgccggttg cattcgattc + 1861 ctgtttgtaa ttgtcctttt aacggcgatc gcgtatttcg tctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/conn q-r.gb b/tools/create_assembly_picklists/test-data/emma_parts/conn q-r.gb new file mode 100644 index 00000000..f1d13062 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/conn q-r.gb @@ -0,0 +1,76 @@ +LOCUS . 1905 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /note="From Exported" + /source="Exported" + misc_feature complement(1154..1245) + /note="conn Q-R" + source complement(1154..1245) + /note="From Exported" + /source="Exported" + misc_feature complement(1251..1256) + /note="BsmBI" + terminator 1323..1354 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1355..1457 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1250..1905 + /note="From Exported" + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcga ccggcttgtt ctgggctagg tgttgaggtt cgattaccac taacgtctga + 1201 gggaaagttg ttgactggac ttgcatgttg atggtggatt atgtcgagcc gagacgaaga + 1261 cgaattctct agatatcgct caatactgac catttaaatc atacctgacc tccatagcag + 1321 aaagtcaaaa gcctccgacc ggaggctttt gacttgatcg gcacgtaaga ggttccaact + 1381 ttcaccataa tgaaataaga tcactaccgg gcgtattttt tgagttatcg agattttcag + 1441 gagctaagga agctaaaatg agccatattc aacgggaaac gtcttgctcg aggccgcgat + 1501 taaattccaa catggatgct gatttatatg ggtataaatg ggctcgcgat aatgtcgggc + 1561 aatcaggtgc gacaatctat cgattgtatg ggaagcccga tgcgccagag ttgtttctga + 1621 aacatggcaa aggtagcgtt gccaatgatg ttacagatga gatggtcagg ctaaactggc + 1681 tgacggaatt tatgcctctt ccgaccatca agcattttat ccgtactcct gatgatgcat + 1741 ggttactcac cactgcgatc ccagggaaaa cagcattcca ggtattagaa gaatatcctg + 1801 attcaggtga aaatattgtt gatgcgctgg cagtgttcct gcgccggttg cattcgattc + 1861 ctgtttgtaa ttgtcctttt aacggcgatc gcgtatttcg tctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/conn r-w.gb b/tools/create_assembly_picklists/test-data/emma_parts/conn r-w.gb new file mode 100644 index 00000000..d1adf3c3 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/conn r-w.gb @@ -0,0 +1,75 @@ +LOCUS . 1853 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /note="From Exported" + /source="Exported" + misc_feature complement(1154..1193) + /note="R-W" + source complement(1154..1193) + /note="From Exported" + /source="Exported" + misc_feature complement(1199..1204) + /note="BsmBI" + terminator 1271..1302 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1303..1405 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1198..1853 + /note="From Exported" + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgt tcggagctgg tagggacttc ggagggcttt gtagttgggt aggaccgcga + 1201 gacgaagacg aattctctag atatcgctca atactgacca tttaaatcat acctgacctc + 1261 catagcagaa agtcaaaagc ctccgaccgg aggcttttga cttgatcggc acgtaagagg + 1321 ttccaacttt caccataatg aaataagatc actaccgggc gtattttttg agttatcgag + 1381 attttcagga gctaaggaag ctaaaatgag ccatattcaa cgggaaacgt cttgctcgag + 1441 gccgcgatta aattccaaca tggatgctga tttatatggg tataaatggg ctcgcgataa + 1501 tgtcgggcaa tcaggtgcga caatctatcg attgtatggg aagcccgatg cgccagagtt + 1561 gtttctgaaa catggcaaag gtagcgttgc caatgatgtt acagatgaga tggtcaggct + 1621 aaactggctg acggaattta tgcctcttcc gaccatcaag cattttatcc gtactcctga + 1681 tgatgcatgg ttactcacca ctgcgatccc agggaaaaca gcattccagg tattagaaga + 1741 atatcctgat tcaggtgaaa atattgttga tgcgctggca gtgttcctgc gccggttgca + 1801 ttcgattcct gtttgtaatt gtccttttaa cggcgatcgc gtatttcgtc tcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/conn t-v.gb b/tools/create_assembly_picklists/test-data/emma_parts/conn t-v.gb new file mode 100644 index 00000000..2147fca1 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/conn t-v.gb @@ -0,0 +1,79 @@ +LOCUS . 1853 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /note="From Exported" + /source="Exported" + misc_feature complement(1154..1193) + /note="conn T-V" + source complement(1154..1193) + /note="From Exported" + /source="Exported" + CDS complement(1189..1191) + /codon_start=1 + /note="STOP" + /translation="" + misc_feature complement(1199..1204) + /note="BsmBI" + terminator 1271..1302 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1303..1405 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1198..1853 + /note="From Exported" + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc aacgggagta tgaagaggcg accaggagga gtgaattatt agccgctcga + 1201 gacgaagacg aattctctag atatcgctca atactgacca tttaaatcat acctgacctc + 1261 catagcagaa agtcaaaagc ctccgaccgg aggcttttga cttgatcggc acgtaagagg + 1321 ttccaacttt caccataatg aaataagatc actaccgggc gtattttttg agttatcgag + 1381 attttcagga gctaaggaag ctaaaatgag ccatattcaa cgggaaacgt cttgctcgag + 1441 gccgcgatta aattccaaca tggatgctga tttatatggg tataaatggg ctcgcgataa + 1501 tgtcgggcaa tcaggtgcga caatctatcg attgtatggg aagcccgatg cgccagagtt + 1561 gtttctgaaa catggcaaag gtagcgttgc caatgatgtt acagatgaga tggtcaggct + 1621 aaactggctg acggaattta tgcctcttcc gaccatcaag cattttatcc gtactcctga + 1681 tgatgcatgg ttactcacca ctgcgatccc agggaaaaca gcattccagg tattagaaga + 1741 atatcctgat tcaggtgaaa atattgttga tgcgctggca gtgttcctgc gccggttgca + 1801 ttcgattcct gtttgtaatt gtccttttaa cggcgatcgc gtatttcgtc tcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/conn w-x.gb b/tools/create_assembly_picklists/test-data/emma_parts/conn w-x.gb new file mode 100644 index 00000000..187dbcb5 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/conn w-x.gb @@ -0,0 +1,76 @@ +LOCUS . 1905 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /note="From Exported" + /source="Exported" + misc_feature complement(1154..1245) + /note="conn W-X" + source complement(1154..1245) + /note="From Exported" + /source="Exported" + misc_feature complement(1251..1256) + /note="BsmBI" + terminator 1323..1354 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1355..1457 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1250..1905 + /note="From Exported" + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc gtgcagatag acaggaagaa tcgacagaac atccgacgaa tagaggacca + 1201 cgggcagcag aagaccatgt ctaaagtgcg agactgaata caagattcgc gagacgaaga + 1261 cgaattctct agatatcgct caatactgac catttaaatc atacctgacc tccatagcag + 1321 aaagtcaaaa gcctccgacc ggaggctttt gacttgatcg gcacgtaaga ggttccaact + 1381 ttcaccataa tgaaataaga tcactaccgg gcgtattttt tgagttatcg agattttcag + 1441 gagctaagga agctaaaatg agccatattc aacgggaaac gtcttgctcg aggccgcgat + 1501 taaattccaa catggatgct gatttatatg ggtataaatg ggctcgcgat aatgtcgggc + 1561 aatcaggtgc gacaatctat cgattgtatg ggaagcccga tgcgccagag ttgtttctga + 1621 aacatggcaa aggtagcgtt gccaatgatg ttacagatga gatggtcagg ctaaactggc + 1681 tgacggaatt tatgcctctt ccgaccatca agcattttat ccgtactcct gatgatgcat + 1741 ggttactcac cactgcgatc ccagggaaaa cagcattcca ggtattagaa gaatatcctg + 1801 attcaggtga aaatattgtt gatgcgctgg cagtgttcct gcgccggttg cattcgattc + 1861 ctgtttgtaa ttgtcctttt aacggcgatc gcgtatttcg tctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/conn w-y.gb b/tools/create_assembly_picklists/test-data/emma_parts/conn w-y.gb new file mode 100644 index 00000000..f6027b24 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/conn w-y.gb @@ -0,0 +1,76 @@ +LOCUS . 1905 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /note="From Exported" + /source="Exported" + misc_feature complement(1154..1245) + /note="conn W-Y" + source complement(1154..1245) + /note="From Exported" + /source="Exported" + misc_feature complement(1251..1256) + /note="BsmBI" + terminator 1323..1354 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1355..1457 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1250..1905 + /note="From Exported" + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc agtgggatgt gtgagtttgt tgagtgaatg gtaattgtgg gagtggtgtg + 1201 ggatttgagg tgtgctggtg tggttgtgac gaggatcaat atgtgttcgc gagacgaaga + 1261 cgaattctct agatatcgct caatactgac catttaaatc atacctgacc tccatagcag + 1321 aaagtcaaaa gcctccgacc ggaggctttt gacttgatcg gcacgtaaga ggttccaact + 1381 ttcaccataa tgaaataaga tcactaccgg gcgtattttt tgagttatcg agattttcag + 1441 gagctaagga agctaaaatg agccatattc aacgggaaac gtcttgctcg aggccgcgat + 1501 taaattccaa catggatgct gatttatatg ggtataaatg ggctcgcgat aatgtcgggc + 1561 aatcaggtgc gacaatctat cgattgtatg ggaagcccga tgcgccagag ttgtttctga + 1621 aacatggcaa aggtagcgtt gccaatgatg ttacagatga gatggtcagg ctaaactggc + 1681 tgacggaatt tatgcctctt ccgaccatca agcattttat ccgtactcct gatgatgcat + 1741 ggttactcac cactgcgatc ccagggaaaa cagcattcca ggtattagaa gaatatcctg + 1801 attcaggtga aaatattgtt gatgcgctgg cagtgttcct gcgccggttg cattcgattc + 1861 ctgtttgtaa ttgtcctttt aacggcgatc gcgtatttcg tctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/conn w-z.gb b/tools/create_assembly_picklists/test-data/emma_parts/conn w-z.gb new file mode 100644 index 00000000..26f1bf72 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/conn w-z.gb @@ -0,0 +1,76 @@ +LOCUS . 1905 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /note="From Exported" + /source="Exported" + misc_feature complement(1154..1245) + /note="conn W-Z" + source complement(1154..1245) + /note="From Exported" + /source="Exported" + misc_feature complement(1251..1256) + /note="BsmBI" + terminator 1323..1354 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1355..1457 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1250..1905 + /note="From Exported" + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgt cgtgggatgt gtgagtttgt tgagtgaatg gtaattgtgg gagtggtgtg + 1201 ggatttgagg tgtgctggtg tggttgtgac gaggatcaat atgtgttcgc gagacgaaga + 1261 cgaattctct agatatcgct caatactgac catttaaatc atacctgacc tccatagcag + 1321 aaagtcaaaa gcctccgacc ggaggctttt gacttgatcg gcacgtaaga ggttccaact + 1381 ttcaccataa tgaaataaga tcactaccgg gcgtattttt tgagttatcg agattttcag + 1441 gagctaagga agctaaaatg agccatattc aacgggaaac gtcttgctcg aggccgcgat + 1501 taaattccaa catggatgct gatttatatg ggtataaatg ggctcgcgat aatgtcgggc + 1561 aatcaggtgc gacaatctat cgattgtatg ggaagcccga tgcgccagag ttgtttctga + 1621 aacatggcaa aggtagcgtt gccaatgatg ttacagatga gatggtcagg ctaaactggc + 1681 tgacggaatt tatgcctctt ccgaccatca agcattttat ccgtactcct gatgatgcat + 1741 ggttactcac cactgcgatc ccagggaaaa cagcattcca ggtattagaa gaatatcctg + 1801 attcaggtga aaatattgtt gatgcgctgg cagtgttcct gcgccggttg cattcgattc + 1861 ctgtttgtaa ttgtcctttt aacggcgatc gcgtatttcg tctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/conn y-z.gb b/tools/create_assembly_picklists/test-data/emma_parts/conn y-z.gb new file mode 100644 index 00000000..bdf738c9 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/conn y-z.gb @@ -0,0 +1,76 @@ +LOCUS . 1905 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /note="From Exported" + /source="Exported" + misc_feature complement(1154..1245) + /note="conn Y-Z" + source complement(1154..1245) + /note="From Exported" + /source="Exported" + misc_feature complement(1251..1256) + /note="BsmBI" + terminator 1323..1354 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1355..1457 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1250..1905 + /note="From Exported" + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgt cgtgggatgt gtgagtttgt tgagtgaatg gtaattgtgg gagtggtgtg + 1201 ggatttgagg tgtgctggtg tggttgtgac gaggatcaat atgtgcagtc gagacgaaga + 1261 cgaattctct agatatcgct caatactgac catttaaatc atacctgacc tccatagcag + 1321 aaagtcaaaa gcctccgacc ggaggctttt gacttgatcg gcacgtaaga ggttccaact + 1381 ttcaccataa tgaaataaga tcactaccgg gcgtattttt tgagttatcg agattttcag + 1441 gagctaagga agctaaaatg agccatattc aacgggaaac gtcttgctcg aggccgcgat + 1501 taaattccaa catggatgct gatttatatg ggtataaatg ggctcgcgat aatgtcgggc + 1561 aatcaggtgc gacaatctat cgattgtatg ggaagcccga tgcgccagag ttgtttctga + 1621 aacatggcaa aggtagcgtt gccaatgatg ttacagatga gatggtcagg ctaaactggc + 1681 tgacggaatt tatgcctctt ccgaccatca agcattttat ccgtactcct gatgatgcat + 1741 ggttactcac cactgcgatc ccagggaaaa cagcattcca ggtattagaa gaatatcctg + 1801 attcaggtga aaatattgtt gatgcgctgg cagtgttcct gcgccggttg cattcgattc + 1861 ctgtttgtaa ttgtcctttt aacggcgatc gcgtatttcg tctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p10_tet-aptazyme.gb b/tools/create_assembly_picklists/test-data/emma_parts/p10_tet-aptazyme.gb new file mode 100644 index 00000000..157c75da --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p10_tet-aptazyme.gb @@ -0,0 +1,75 @@ +LOCUS . 1984 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1185..1312 + /note="Tet-Aptazyme" + source 1154..1324 + /source="Exported" + misc_feature complement(1330..1335) + /note="BsmBI" + terminator 1402..1433 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1434..1536 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1329..1984 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgt gctagacaat acaggaagga accaaacaaa caaaggcgaa agccggcgcg + 1201 tcctggattc cacgtacaaa aacataccag atttcgatct ggagaggtga agaatacgac + 1261 caccttgtac ggtacatcca gctgatgagt cccaaatagg acgaaacgcg ctcaaacaaa + 1321 caaaggtacg agacgaagac gaattctcta gatatcgctc aatactgacc atttaaatca + 1381 tacctgacct ccatagcaga aagtcaaaag cctccgaccg gaggcttttg acttgatcgg + 1441 cacgtaagag gttccaactt tcaccataat gaaataagat cactaccggg cgtatttttt + 1501 gagttatcga gattttcagg agctaaggaa gctaaaatga gccatattca acgggaaacg + 1561 tcttgctcga ggccgcgatt aaattccaac atggatgctg atttatatgg gtataaatgg + 1621 gctcgcgata atgtcgggca atcaggtgcg acaatctatc gattgtatgg gaagcccgat + 1681 gcgccagagt tgtttctgaa acatggcaaa ggtagcgttg ccaatgatgt tacagatgag + 1741 atggtcaggc taaactggct gacggaattt atgcctcttc cgaccatcaa gcattttatc + 1801 cgtactcctg atgatgcatg gttactcacc actgcgatcc cagggaaaac agcattccag + 1861 gtattagaag aatatcctga ttcaggtgaa aatattgttg atgcgctggc agtgttcctg + 1921 cgccggttgc attcgattcc tgtttgtaat tgtcctttta acggcgatcg cgtatttcgt + 1981 ctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p11_sv40polya.gb b/tools/create_assembly_picklists/test-data/emma_parts/p11_sv40polya.gb new file mode 100644 index 00000000..29f1d7c9 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p11_sv40polya.gb @@ -0,0 +1,74 @@ +LOCUS . 1944 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + misc_feature 1814..1944 + /note="SV40 polyA" + source 1814..1944 + /source="Exported" +ORIGIN + 1 cgtccgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcgg gtaacttgtt tattgcagct tataatggtt acaaataaag caatagcatc + 1861 acaaatttca caaataaagc atttttttca ctgcattcta gttgtggttt gtccaaactc + 1921 atcaatgtat cttatcatgt ctgt +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p14_cmvp.gb b/tools/create_assembly_picklists/test-data/emma_parts/p14_cmvp.gb new file mode 100644 index 00000000..723edf06 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p14_cmvp.gb @@ -0,0 +1,86 @@ +LOCUS . 2356 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1144..1149 + /note="BsmBI" + source 5..1150 + /source="Exported" + source complement(1155..1697) + /source="Exported" + promoter complement(1191..1393) + /note="CMV promoter" + /note="human cytomegalovirus (CMV) immediate early + promoter" + enhancer complement(1394..1696) + /note="CMV enhancer" + /note="human cytomegalovirus immediate early enhancer" + misc_feature complement(1703..1708) + /note="BsmBI" + terminator 1774..1805 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1806..1908 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1702..2356 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tttcgtctcg ttgccagatc tcctcggtac cggatccagt cgacgaatta gctctgctta + 1201 tatagacctc ccaccgtaca cgcctaccgc ccatttgcgt caatggggcg gagttgttac + 1261 gacattttgg aaagtcccgt tgattttggt gccaaaacaa actcccattg acgtcaatgg + 1321 ggtggagact tggaaatccc cgtgagtcaa accgctatcc acgcccattg atgtactgcc + 1381 aaaaccgcat caccatggta atagcgatga ctaatacgta gatgtactgc caagtaggaa + 1441 agtcccataa ggtcatgtac tgggcataat gccaggcggg ccatttaccg tcattgacgt + 1501 caataggggg cgtacttggc atatgataca cttgatgtac tgccaagtgg gcagtttacc + 1561 gtaaatactc cacccattga cgtcaatgga aagtccctat tggcgttact atgggaacat + 1621 acgtcattat tgacgtcaat gggcgggggt cgttgggcgg tcagccaggc gggccattta + 1681 ccgtaagtta tgtaacggta gcgagacgtg acgaattctc tagatatcgc tcaatactga + 1741 ccatttaaat catacctgac ctccatagca gaaagtcaaa agcctccgac cggaggcttt + 1801 tgacttgatc ggcacgtaag aggttccaac tttcaccata atgaaataag atcactaccg + 1861 ggcgtatttt ttgagttatc gagattttca ggagctaagg aagctaaaat gagccatatt + 1921 caacgggaaa cgtcttgctc gaggccgcga ttaaattcca acatggatgc tgatttatat + 1981 gggtataaat gggctcgcga taatgtcggg caatcaggtg cgacaatcta tcgattgtat + 2041 gggaagcccg atgcgccaga gttgtttctg aaacatggca aaggtagcgt tgccaatgat + 2101 gttacagatg agatggtcag gctaaactgg ctgacggaat ttatgcctct tccgaccatc + 2161 aagcatttta tccgtactcc tgatgatgca tggttactca ccactgcgat cccagggaaa + 2221 acagcattcc aggtattaga agaatatcct gattcaggtg aaaatattgt tgatgcgctg + 2281 gcagtgttcc tgcgccggtt gcattcgatt cctgtttgta attgtccttt taacggcgat + 2341 cgcgtatttc gtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p14_sv40p.gb b/tools/create_assembly_picklists/test-data/emma_parts/p14_sv40p.gb new file mode 100644 index 00000000..bf0cbd43 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p14_sv40p.gb @@ -0,0 +1,82 @@ +LOCUS . 2193 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1144..1149 + /note="BsmBI" + source 5..1150 + /source="Exported" + source complement(1155..1534) + /source="Exported" + promoter complement(1205..1534) + /note="SV40 promoter" + /note="SV40 enhancer and early promoter" + rep_origin complement(1219..1354) + /note="SV40 ori" + /note="SV40 origin of replication" + misc_feature complement(1540..1545) + /note="BsmBI" + terminator 1611..1642 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1643..1745 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1539..2193 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tttcgtctcg ttgccctgtc tcttgatcag atccgaaaat ggatatacaa gctcccggga + 1201 gctttttgca aaagcctagg cctccaaaaa agcctcctca ctacttctgg aatagctcag + 1261 aggcagaggc ggcctcggcc tctgcataaa taaaaaaaat tagtcagcca tggggcggag + 1321 aatgggcgga actgggcgga gttaggggcg ggatgggcgg agttaggggc gggactatgg + 1381 ttgctgacta attgagatgc atgctttgca tacttctgcc tgctggggag cctggggact + 1441 ttccacacct ggttgctgac taattgagat gcatgctttg catacttctg cctgctgggg + 1501 agcctgggga ctttccacac cctaactgac acacgtagcg agacgtgacg aattctctag + 1561 atatcgctca atactgacca tttaaatcat acctgacctc catagcagaa agtcaaaagc + 1621 ctccgaccgg aggcttttga cttgatcggc acgtaagagg ttccaacttt caccataatg + 1681 aaataagatc actaccgggc gtattttttg agttatcgag attttcagga gctaaggaag + 1741 ctaaaatgag ccatattcaa cgggaaacgt cttgctcgag gccgcgatta aattccaaca + 1801 tggatgctga tttatatggg tataaatggg ctcgcgataa tgtcgggcaa tcaggtgcga + 1861 caatctatcg attgtatggg aagcccgatg cgccagagtt gtttctgaaa catggcaaag + 1921 gtagcgttgc caatgatgtt acagatgaga tggtcaggct aaactggctg acggaattta + 1981 tgcctcttcc gaccatcaag cattttatcc gtactcctga tgatgcatgg ttactcacca + 2041 ctgcgatccc agggaaaaca gcattccagg tattagaaga atatcctgat tcaggtgaaa + 2101 atattgttga tgcgctggca gtgttcctgc gccggttgca ttcgattcct gtttgtaatt + 2161 gtccttttaa cggcgatcgc gtatttcgtc tcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p15_puror.gb b/tools/create_assembly_picklists/test-data/emma_parts/p15_puror.gb new file mode 100644 index 00000000..c715d70e --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p15_puror.gb @@ -0,0 +1,96 @@ +LOCUS . 2424 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1154..1161 + /note="KozaK" + CDS 1162..1164 + /codon_start=1 + /note="ATG" + /translation="M" + CDS 1165..1761 + /codon_start=1 + /gene="pac from Streptomyces" + /note="PuroR" + /note="confers resistance to puromycin" + /product="puromycin N-acetyltransferase" + /translation="TEYKPTVRLATRDDVPRAVRTLAAAFADYPATRHTVDPDRHIERV + TELQELFLTRVGLDIGKVWVADDGAAVAVWTTPESVEAGAVFAEIGPRMAELSGSRLAA + QQQMEGLLAPHRPKEPAWFLATVGVSPDHQGKGLGSAVVLPGVEAAERAGVPAFLETSA + PRNLPFYERLGFTVTADVECPKDRATWCMTRKPGA" + source 1154..1764 + /source="Exported" + misc_feature complement(1770..1775) + /note="BsmBI" + terminator 1842..1873 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1874..1976 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1769..2424 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgg caaccgccac catgaccgag tacaagccca cggtgcgcct cgccacccgc + 1201 gacgacgtcc ccagggccgt acgcaccctc gccgccgcgt tcgccgacta ccccgccacg + 1261 cgccacaccg tcgatccgga ccgccacatc gagcgggtca ccgagctgca agaactcttc + 1321 ctcacgcgcg tcgggctcga catcggcaag gtgtgggtcg cggacgacgg cgccgcggtg + 1381 gcggtctgga ccacgccgga gagcgtcgaa gcgggggcgg tgttcgccga gatcggcccg + 1441 cgcatggccg agttgagcgg ttcccggctg gccgcgcagc aacagatgga aggcctcctg + 1501 gcgccgcacc ggcccaagga gcccgcgtgg ttcctggcca ccgtcggcgt gtcgcccgac + 1561 caccagggca agggtctggg cagcgccgtc gtgctccccg gagtggaggc ggccgagcgc + 1621 gccggggtgc ccgccttcct ggaaacctcc gcgccccgca acctcccctt ctacgagcgg + 1681 ctcggcttca ccgtcaccgc cgacgtcgag tgcccgaagg accgcgcgac ctggtgcatg + 1741 acccgcaagc ccggtgccta ataaccctcg agacgaagac gaattctcta gatatcgctc + 1801 aatactgacc atttaaatca tacctgacct ccatagcaga aagtcaaaag cctccgaccg + 1861 gaggcttttg acttgatcgg cacgtaagag gttccaactt tcaccataat gaaataagat + 1921 cactaccggg cgtatttttt gagttatcga gattttcagg agctaaggaa gctaaaatga + 1981 gccatattca acgggaaacg tcttgctcga ggccgcgatt aaattccaac atggatgctg + 2041 atttatatgg gtataaatgg gctcgcgata atgtcgggca atcaggtgcg acaatctatc + 2101 gattgtatgg gaagcccgat gcgccagagt tgtttctgaa acatggcaaa ggtagcgttg + 2161 ccaatgatgt tacagatgag atggtcaggc taaactggct gacggaattt atgcctcttc + 2221 cgaccatcaa gcattttatc cgtactcctg atgatgcatg gttactcacc actgcgatcc + 2281 cagggaaaac agcattccag gtattagaag aatatcctga ttcaggtgaa aatattgttg + 2341 atgcgctggc agtgttcctg cgccggttgc attcgattcc tgtttgtaat tgtcctttta + 2401 acggcgatcg cgtatttcgt ctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p16_bghpolya.gb b/tools/create_assembly_picklists/test-data/emma_parts/p16_bghpolya.gb new file mode 100644 index 00000000..11e0a13e --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p16_bghpolya.gb @@ -0,0 +1,77 @@ +LOCUS . 2070 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + polyA_signal 1186..1410 + /note="bGH poly(A) signal" + /note="bovine growth hormone polyadenylation signal" + source 1154..1410 + /source="Exported" + misc_feature complement(1416..1421) + /note="BsmBI" + terminator 1488..1519 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1520..1622 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1415..2070 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc cctctctggg gttcgaaatg accgaccaag cgacgctgtg ccttctagtt + 1201 gccagccatc tgttgtttgc ccctcccccg tgccttcctt gaccctggaa ggtgccactc + 1261 ccactgtcct ttcctaataa aatgaggaaa ttgcatcgca ttgtctgagt aggtgtcatt + 1321 ctattctggg gggtggggtg gggcaggaca gcaaggggga ggattgggaa gacaatagca + 1381 ggcatgctgg ggatgcggtg ggctctatgg gctccgagac gaagacgaat tctctagata + 1441 tcgctcaata ctgaccattt aaatcatacc tgacctccat agcagaaagt caaaagcctc + 1501 cgaccggagg cttttgactt gatcggcacg taagaggttc caactttcac cataatgaaa + 1561 taagatcact accgggcgta ttttttgagt tatcgagatt ttcaggagct aaggaagcta + 1621 aaatgagcca tattcaacgg gaaacgtctt gctcgaggcc gcgattaaat tccaacatgg + 1681 atgctgattt atatgggtat aaatgggctc gcgataatgt cgggcaatca ggtgcgacaa + 1741 tctatcgatt gtatgggaag cccgatgcgc cagagttgtt tctgaaacat ggcaaaggta + 1801 gcgttgccaa tgatgttaca gatgagatgg tcaggctaaa ctggctgacg gaatttatgc + 1861 ctcttccgac catcaagcat tttatccgta ctcctgatga tgcatggtta ctcaccactg + 1921 cgatcccagg gaaaacagca ttccaggtat tagaagaata tcctgattca ggtgaaaata + 1981 ttgttgatgc gctggcagtg ttcctgcgcc ggttgcattc gattcctgtt tgtaattgtc + 2041 cttttaacgg cgatcgcgta tttcgtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p18_cmvp.gb b/tools/create_assembly_picklists/test-data/emma_parts/p18_cmvp.gb new file mode 100644 index 00000000..64d77421 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p18_cmvp.gb @@ -0,0 +1,86 @@ +LOCUS . 2356 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + enhancer 1155..1457 + /note="CMV enhancer" + /note="human cytomegalovirus immediate early enhancer" + promoter 1458..1660 + /note="CMV promoter" + /note="human cytomegalovirus (CMV) immediate early + promoter" + source 1154..1696 + /source="Exported" + misc_feature complement(1702..1707) + /note="BsmBI" + terminator 1774..1805 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1806..1908 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1701..2356 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc ggtcgttaca taacttacgg taaatggccc gcctggctga ccgcccaacg + 1201 acccccgccc attgacgtca ataatgacgt atgttcccat agtaacgcca atagggactt + 1261 tccattgacg tcaatgggtg gagtatttac ggtaaactgc ccacttggca gtacatcaag + 1321 tgtatcatat gccaagtacg ccccctattg acgtcaatga cggtaaatgg cccgcctggc + 1381 attatgccca gtacatgacc ttatgggact ttcctacttg gcagtacatc tacgtattag + 1441 tcatcgctat taccatggtg atgcggtttt ggcagtacat caatgggcgt ggatagcggt + 1501 ttgactcacg gggatttcca agtctccacc ccattgacgt caatgggagt ttgttttggc + 1561 accaaaatca acgggacttt ccaaaatgtc gtaacaactc cgccccattg acgcaaatgg + 1621 gcggtaggcg tgtacggtgg gaggtctata taagcagagc taattcgtcg actggatccg + 1681 gtaccgagga gatctggtgc cgagacgaag acgaattctc tagatatcgc tcaatactga + 1741 ccatttaaat catacctgac ctccatagca gaaagtcaaa agcctccgac cggaggcttt + 1801 tgacttgatc ggcacgtaag aggttccaac tttcaccata atgaaataag atcactaccg + 1861 ggcgtatttt ttgagttatc gagattttca ggagctaagg aagctaaaat gagccatatt + 1921 caacgggaaa cgtcttgctc gaggccgcga ttaaattcca acatggatgc tgatttatat + 1981 gggtataaat gggctcgcga taatgtcggg caatcaggtg cgacaatcta tcgattgtat + 2041 gggaagcccg atgcgccaga gttgtttctg aaacatggca aaggtagcgt tgccaatgat + 2101 gttacagatg agatggtcag gctaaactgg ctgacggaat ttatgcctct tccgaccatc + 2161 aagcatttta tccgtactcc tgatgatgca tggttactca ccactgcgat cccagggaaa + 2221 acagcattcc aggtattaga agaatatcct gattcaggtg aaaatattgt tgatgcgctg + 2281 gcagtgttcc tgcgccggtt gcattcgatt cctgtttgta attgtccttt taacggcgat + 2341 cgcgtatttc gtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p18_ef1ap.gb b/tools/create_assembly_picklists/test-data/emma_parts/p18_ef1ap.gb new file mode 100644 index 00000000..a34b7e84 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p18_ef1ap.gb @@ -0,0 +1,98 @@ +LOCUS . 3037 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + promoter 5..1183 + /note="EF-1-alpha promoter" + /note="strong constitutive promoter for human elongation + factor EF-1-alpha" + intron 236..1174 + /note="EF-1-alpha intron A" + /note="intron upstream of the start codon of human + EF-1-alpha" + source 5..1228 + /source="Exported" + misc_feature complement(1234..1239) + /note="BsmBI" + terminator 1306..1337 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1338..1440 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1233..1888 + /source="Exported" + terminator 2280..2307 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(2319..2906) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 2928..2957 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 3031..3036 + /note="BsmBI" + source 1893..3037 + /source="Exported" +ORIGIN + 1 cggtggctcc ggtgcccgtc agtgggcaga gcgcacatcg cccacagtcc ccgagaagtt + 61 ggggggaggg gtcggcaatt gaaccggtgc ctagagaagg tggcgcgggg taaactggga + 121 aagtgatgtc gtgtactggc tccgcctttt tcccgagggt gggggagaac cgtatataag + 181 tgcagtagtc gccgtgaacg ttctttttcg caacgggttt gccgccagaa cacaggtaag + 241 tgccgtgtgt ggttcccgcg ggcctggcct ctttacgggt tatggccctt gcgtgccttg + 301 aattacttcc acctggctgc agtacgtgat tcttgatccc gagcttcggg ttggaagtgg + 361 gtgggagagt tcgaggcctt gcgcttaagg agccccttcg cctcgtgctt gagttgaggc + 421 ctggcctggg cgctggggcc gccgcgtgcg aatctggtgg caccttcgcg cctgtctcgc + 481 tgctttcgat aagtctctag ccatttaaaa tttttgatga cctgctgcga cgcttttttt + 541 ctggcaagat agtcttgtaa atgcgggcca agatctgcac actggtattt cggtttttgg + 601 ggccgcgggc ggcgacgggg cccgtgcgtc ccagcgcaca tgttcggcga ggcggggcct + 661 gcgagcgcgg ccaccgagaa tcggacgggg gtagtctcaa gctggccggc ctgctctggt + 721 gcctggcctc gcgccgccgt gtatcgcccc gccctgggcg gcaaggctgg cccggtcggc + 781 accagttgcg tgagcggaaa gatggccgct tcccggccct gctgcaggga gctcaaaatg + 841 gaggacgcgg cgctcgggag agcgggcggg tgagtcaccc acacaaagga aaagggcctt + 901 tccgtcctca gccgtcgctt catgtgactc cacggagtac cgggcgccgt ccaggcacct + 961 cgattagttc tcgagctttt ggagtacgtc gtctttaggt tggggggagg ggttttatgc + 1021 gatggagttt ccccacactg agtgggtgga gactgaagtt aggccagctt ggcacttgat + 1081 gtaattctcc ttggaatttg ccctttttga gtttggatct tggttcattc tcaagcctca + 1141 gacagtggtt caaagttttt ttcttccatt tcaggtgtcg tgacgctagc gctaccggac + 1201 tcagatctcg agctcaagct tcgaattcgt gccgagacga agacgaattc tctagatatc + 1261 gctcaatact gaccatttaa atcatacctg acctccatag cagaaagtca aaagcctccg + 1321 accggaggct tttgacttga tcggcacgta agaggttcca actttcacca taatgaaata + 1381 agatcactac cgggcgtatt ttttgagtta tcgagatttt caggagctaa ggaagctaaa + 1441 atgagccata ttcaacggga aacgtcttgc tcgaggccgc gattaaattc caacatggat + 1501 gctgatttat atgggtataa atgggctcgc gataatgtcg ggcaatcagg tgcgacaatc + 1561 tatcgattgt atgggaagcc cgatgcgcca gagttgtttc tgaaacatgg caaaggtagc + 1621 gttgccaatg atgttacaga tgagatggtc aggctaaact ggctgacgga atttatgcct + 1681 cttccgacca tcaagcattt tatccgtact cctgatgatg catggttact caccactgcg + 1741 atcccaggga aaacagcatt ccaggtatta gaagaatatc ctgattcagg tgaaaatatt + 1801 gttgatgcgc tggcagtgtt cctgcgccgg ttgcattcga ttcctgtttg taattgtcct + 1861 tttaacggcg atcgcgtatt tcgtctcgct caggcgcaat cacgaatgaa taacggtttg + 1921 gttggtgcga gtgattttga tgacgagcgt aatggctggc ctgttgaaca agtctggaaa + 1981 gaaatgcata agcttttgcc attctcaccg gattcagtcg tcactcatgg tgatttctca + 2041 cttgataacc ttatttttga cgaggggaaa ttaataggtt gtattgatgt tggacgagtc + 2101 ggaatcgcag accgatacca ggatcttgcc atcctatgga actgcctcgg tgagttttct + 2161 ccttcattac agaaacggct ttttcaaaaa tatggtattg ataatcctga tatgaataaa + 2221 ttgcagtttc acttgatgct cgatgagttt ttctaatgag ggcccaaatg taatcacctg + 2281 gctcaccttc gggtgggcct ttctgcgttg ctggcgtttt tccataggct ccgcccccct + 2341 gacgagcatc acaaaaatcg atgctcaagt cagaggtggc gaaacccgac aggactataa + 2401 agataccagg cgtttccccc tggaagctcc ctcgtgcgct ctcctgttcc gaccctgccg + 2461 cttaccggat acctgtccgc ctttctccct tcgggaagcg tggcgctttc tcatagctca + 2521 cgctgtaggt atctcagttc ggtgtaggtc gttcgctcca agctgggctg tgtgcacgaa + 2581 ccccccgttc agcccgaccg ctgcgcctta tccggtaact atcgtcttga gtccaacccg + 2641 gtaagacacg acttatcgcc actggcagca gccactggta acaggattag cagagcgagg + 2701 tatgtaggcg gtgctacaga gttcttgaag tggtggccta actacggcta cactagaaga + 2761 acagtatttg gtatctgcgc tctgctgaag ccagttacct cggaaaaaga gttggtagct + 2821 cttgatccgg caaacaaacc accgctggta gcggtggttt ttttgtttgc aagcagcaga + 2881 ttacgcgcag aaaaaaagga tctcaagaag atcctttgat tttctaccga agaaaggccc + 2941 acccgtgaag gtgagccagt gagttgattg cagtccagtt acgctggagt ctgaggctcg + 3001 tcctgaatga tatcaagctt gaattcgtta cgtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p19_mneogreen.gb b/tools/create_assembly_picklists/test-data/emma_parts/p19_mneogreen.gb new file mode 100644 index 00000000..b5fff6e0 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p19_mneogreen.gb @@ -0,0 +1,98 @@ +LOCUS . 2529 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1154..1164 + /note="KozaK" + CDS 1162..1164 + /codon_start=1 + /note="ATG" + /translation="M" + CDS 1165..1869 + /codon_start=1 + /note="mNeonGreen" + /product="bright monomeric yellow-green fluorescent protein + derived from LanYFP (Shaner et al., 2013)" + /translation="VSKGEEDNMASLPATHELHIFGSINGVDFDMVGQGTGNPNDGYEE + LNLKSTKGDLQFSPWILVPHIGYGFHQYLPYPDGMSPFQAAMVDGSGYQVHRTMQFEDG + ASLTVNYRYTYEGSHIKGEAQVKGTGFPADGPVMTNSLTAADWCRSKKTYPNDKTIIST + FKWSYTTGNGKRYRSTARTTYTFAKPMAANYLKNQPMYVFRKTELKHSKTELNFKEWQK + AFTDVMGMDELYK" + source 1154..1869 + /source="Exported" + misc_feature complement(1875..1880) + /note="BsmBI" + terminator 1947..1978 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1979..2081 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1874..2529 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgg tgcccgccac catggtgagc aagggcgagg aggataacat ggcctctctc + 1201 ccagcgacac atgagttaca catctttggc tccatcaacg gtgtggactt tgacatggtg + 1261 ggtcagggca ccggcaatcc aaatgatggt tatgaggagt taaacctgaa gtccaccaag + 1321 ggtgacctcc agttctcccc ctggattctg gtccctcata tcgggtatgg cttccatcag + 1381 tacctgccct accctgacgg gatgtcgcct ttccaggccg ccatggtaga tggctccgga + 1441 taccaagtcc atcgcacaat gcagtttgaa gatggtgcct cccttactgt taactaccgc + 1501 tacacctacg agggaagcca catcaaagga gaggcccagg tgaaggggac tggtttccct + 1561 gctgacggtc ctgtgatgac caactcgctg accgctgcgg actggtgcag gtcgaagaag + 1621 acttacccca acgacaaaac catcatcagt acctttaagt ggagttacac cactggaaat + 1681 ggcaagcgct accggagcac tgcgcggacc acctacacct ttgccaagcc aatggcggct + 1741 aactatctga agaaccagcc gatgtacgtg ttccgtaaga cggagctcaa gcactccaag + 1801 accgagctca acttcaagga gtggcaaaag gcctttaccg atgtgatggg catggacgag + 1861 ctgtacaaga gcgcgagacg aagacgaatt ctctagatat cgctcaatac tgaccattta + 1921 aatcatacct gacctccata gcagaaagtc aaaagcctcc gaccggaggc ttttgacttg + 1981 atcggcacgt aagaggttcc aactttcacc ataatgaaat aagatcacta ccgggcgtat + 2041 tttttgagtt atcgagattt tcaggagcta aggaagctaa aatgagccat attcaacggg + 2101 aaacgtcttg ctcgaggccg cgattaaatt ccaacatgga tgctgattta tatgggtata + 2161 aatgggctcg cgataatgtc gggcaatcag gtgcgacaat ctatcgattg tatgggaagc + 2221 ccgatgcgcc agagttgttt ctgaaacatg gcaaaggtag cgttgccaat gatgttacag + 2281 atgagatggt caggctaaac tggctgacgg aatttatgcc tcttccgacc atcaagcatt + 2341 ttatccgtac tcctgatgat gcatggttac tcaccactgc gatcccaggg aaaacagcat + 2401 tccaggtatt agaagaatat cctgattcag gtgaaaatat tgttgatgcg ctggcagtgt + 2461 tcctgcgccg gttgcattcg attcctgttt gtaattgtcc ttttaacggc gatcgcgtat + 2521 ttcgtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p19_mruby2.gb b/tools/create_assembly_picklists/test-data/emma_parts/p19_mruby2.gb new file mode 100644 index 00000000..1d65e8a8 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p19_mruby2.gb @@ -0,0 +1,99 @@ +LOCUS . 2532 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1154..1164 + /note="KozaK" + CDS 1162..1164 + /codon_start=1 + /note="ATG" + /translation="M" + CDS 1165..1872 + /codon_start=1 + /note="mRuby2" + /product="monomeric red fluorescent protein derived from + mRuby, with improved photophysical properties (Lam et al., + 2012)" + /translation="VSKGEELIKENMRMKVVMEGSVNGHQFKCTGEGEGNPYMGTQTMR + IKVIEGGPLPFAFDILATSFMYGSRTFIKYPKGIPDFFKQSFPEGFTWERVTRYEDGGV + VTVMQDTSLEDGCLVYHVQVRGVNFPSNGPVMQKKTKGWEPNTEMMYPADGGLRGYTHM + ALKVDGGGHLSCSFVTTYRSKKTVGNIKMPGIHAVDHRLERLEESDNEMFVVQREHAVA + KFAGLGGGMDELYK" + source 1154..1872 + /source="Exported" + misc_feature complement(1878..1883) + /note="BsmBI" + terminator 1950..1981 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1982..2084 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1877..2532 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgg tgcccgccac catggtgtct aagggcgaag agctgatcaa ggaaaatatg + 1201 cgtatgaagg tggtcatgga aggttcggtc aacggccacc aattcaaatg cacaggtgaa + 1261 ggagaaggca atccgtacat gggaactcaa accatgagga tcaaagtcat cgagggagga + 1321 cccctgccat ttgcctttga cattcttgcc acgtcgttca tgtatggcag ccgtactttt + 1381 atcaagtacc cgaaaggcat tcctgatttc tttaaacagt cctttcctga gggttttact + 1441 tgggaaagag ttacgagata cgaagatggt ggagtcgtca ccgtcatgca ggacaccagc + 1501 cttgaggatg gctgtctcgt ttaccacgtc caagtcagag gggtaaactt tccctccaat + 1561 ggtcccgtga tgcagaagaa gaccaagggt tgggagccta atacagagat gatgtatcca + 1621 gcagatggtg gtctgagggg atacactcat atggcactga aagttgatgg tggtggccat + 1681 ctgtcttgct ctttcgtaac aacttacagg tcaaaaaaga ccgtcgggaa catcaagatg + 1741 cccggtatcc atgccgttga tcaccgcctg gaaaggttag aggaaagtga caatgaaatg + 1801 ttcgtagtac aacgcgaaca cgcagttgcc aagttcgccg ggcttggtgg tgggatggac + 1861 gagctgtaca agagcgcgag acgaagacga attctctaga tatcgctcaa tactgaccat + 1921 ttaaatcata cctgacctcc atagcagaaa gtcaaaagcc tccgaccgga ggcttttgac + 1981 ttgatcggca cgtaagaggt tccaactttc accataatga aataagatca ctaccgggcg + 2041 tattttttga gttatcgaga ttttcaggag ctaaggaagc taaaatgagc catattcaac + 2101 gggaaacgtc ttgctcgagg ccgcgattaa attccaacat ggatgctgat ttatatgggt + 2161 ataaatgggc tcgcgataat gtcgggcaat caggtgcgac aatctatcga ttgtatggga + 2221 agcccgatgc gccagagttg tttctgaaac atggcaaagg tagcgttgcc aatgatgtta + 2281 cagatgagat ggtcaggcta aactggctga cggaatttat gcctcttccg accatcaagc + 2341 attttatccg tactcctgat gatgcatggt tactcaccac tgcgatccca gggaaaacag + 2401 cattccaggt attagaagaa tatcctgatt caggtgaaaa tattgttgat gcgctggcag + 2461 tgttcctgcg ccggttgcat tcgattcctg tttgtaattg tccttttaac ggcgatcgcg + 2521 tatttcgtct cg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p19_mtagbfp2.gb b/tools/create_assembly_picklists/test-data/emma_parts/p19_mtagbfp2.gb new file mode 100644 index 00000000..15298234 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p19_mtagbfp2.gb @@ -0,0 +1,99 @@ +LOCUS . 2532 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1154..1164 + /note="KozaK" + CDS 1162..1164 + /codon_start=1 + /note="ATG" + /translation="M" + CDS 1165..1872 + /codon_start=1 + /note="mTagBFP2" + /note="mammalian codon-optimized" + /product="enhanced monomeric blue fluorescent protein + (Subach et al., 2011)" + /translation="VSKGEELIKENMHMKLYMEGTVDNHHFKCTSEGEGKPYEGTQTMR + IKVVEGGPLPFAFDILATSFLYGSKTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGV + LTATQDTSLQDGCLIYNVKIRGVNFTSNGPVMQKKTLGWEAFTETLYPADGGLEGRNDM + ALKLVGGSHLIANAKTTYRSKKPAKNLKMPGVYYVDYRLERIKEANNETYVEQHEVAVA + RYCDLPSKLGHKLN" + source 1154..1872 + /source="Exported" + misc_feature complement(1878..1883) + /note="BsmBI" + terminator 1950..1981 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1982..2084 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1877..2532 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgg tgcccgccac catggtgtct aagggcgaag agctgattaa ggagaacatg + 1201 cacatgaagc tgtacatgga gggcaccgtg gacaaccatc acttcaagtg cacatccgag + 1261 ggcgaaggca agccctacga gggcacccag accatgagaa tcaaggtggt cgagggcggc + 1321 cctctcccct tcgccttcga catcctggct actagcttcc tctacggcag caagaccttc + 1381 atcaaccaca cccagggcat ccccgacttc ttcaagcagt ccttccctga gggcttcaca + 1441 tgggagagag tcaccacata cgaagacggg ggcgtgctga ccgctaccca ggacaccagc + 1501 ctccaggacg gctgcctcat ctacaacgtc aagatcagag gggtgaactt cacatccaac + 1561 ggccctgtga tgcagaagaa aacactcggc tgggaggcct tcaccgaaac gctgtacccc + 1621 gctgacggcg gcctggaagg cagaaacgac atggccctga agctcgtggg cgggagccat + 1681 ctgatcgcaa acgccaagac cacatataga tccaagaaac ccgctaagaa cctcaagatg + 1741 cctggcgtct actatgtgga ctacagactg gaaagaatca aggaggccaa caacgaaacc + 1801 tacgtcgagc agcacgaggt ggcagtggcc agatactgcg acctccctag caaactgggg + 1861 cacaagctta atagcgcgag acgaagacga attctctaga tatcgctcaa tactgaccat + 1921 ttaaatcata cctgacctcc atagcagaaa gtcaaaagcc tccgaccgga ggcttttgac + 1981 ttgatcggca cgtaagaggt tccaactttc accataatga aataagatca ctaccgggcg + 2041 tattttttga gttatcgaga ttttcaggag ctaaggaagc taaaatgagc catattcaac + 2101 gggaaacgtc ttgctcgagg ccgcgattaa attccaacat ggatgctgat ttatatgggt + 2161 ataaatgggc tcgcgataat gtcgggcaat caggtgcgac aatctatcga ttgtatggga + 2221 agcccgatgc gccagagttg tttctgaaac atggcaaagg tagcgttgcc aatgatgtta + 2281 cagatgagat ggtcaggcta aactggctga cggaatttat gcctcttccg accatcaagc + 2341 attttatccg tactcctgat gatgcatggt tactcaccac tgcgatccca gggaaaacag + 2401 cattccaggt attagaagaa tatcctgatt caggtgaaaa tattgttgat gcgctggcag + 2461 tgttcctgcg ccggttgcat tcgattcctg tttgtaattg tccttttaac ggcgatcgcg + 2521 tatttcgtct cg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p19_tet-on-3g.gb b/tools/create_assembly_picklists/test-data/emma_parts/p19_tet-on-3g.gb new file mode 100644 index 00000000..a09820ac --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p19_tet-on-3g.gb @@ -0,0 +1,95 @@ +LOCUS . 2574 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1154..1161 + /note="Kozak" + CDS 1162..1908 + /codon_start=1 + /note="Tet-On(R) 3G" + /product="modified rtTA protein that binds tightly to + promoters containing the tet operator in the presence of + doxycycline" + /translation="MSRLDKSKVINSALELLNGVGIEGLTTRKLAQKLGVEQPTLYWHV + KNKRALLDALPIEMLDRHHTHSCPLEGESWQDFLRNNAKSYRCALLSHRDGAKVHLGTR + PTEKQYETLENQLAFLCQQGFSLENALYALSAVGHFTLGCVLEEQEHQVAKEERETPTT + DSMPPLLKQAIELFDRQGAEPAFLFGLELIICGLEKQLKCESGGPTDALDDFDLDMLPA + DALDDFDLDMLPADALDDFDLDMLPGS" + source 1154..1914 + /source="Exported" + misc_feature complement(1920..1925) + /note="BsmBI" + terminator 1992..2023 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 2024..2126 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1919..2574 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgg tgcccgccac catgtctaga ctggacaaga gcaaagtcat aaactctgct + 1201 ctggaattac tcaatggagt cggtatcgaa ggcctgacga caaggaaact cgctcaaaag + 1261 ctgggagttg agcagcctac cctgtactgg cacgtgaaga acaagcgggc cctgctcgat + 1321 gccctgccaa tcgagatgct ggacaggcat catacccact cctgccccct ggaaggcgag + 1381 tcatggcaag actttctgcg gaacaacgcc aagtcatacc gctgtgctct cctctcacat + 1441 cgcgacgggg ctaaagtgca tctcggcacc cgcccaacag agaaacagta cgaaaccctg + 1501 gaaaatcagc tcgcgttcct gtgtcagcaa ggcttctccc tggagaacgc actgtacgct + 1561 ctgtccgccg tgggccactt tacactgggc tgcgtattgg aggaacagga gcatcaagta + 1621 gcaaaagagg aaagagagac acctaccacc gattctatgc ccccacttct gaaacaagca + 1681 attgagctgt tcgaccggca gggagccgaa cctgccttcc ttttcggcct ggaactaatc + 1741 atatgtggcc tggagaaaca gctaaagtgc gaaagcggcg ggccgaccga cgcccttgac + 1801 gattttgact tagacatgct cccagccgat gcccttgacg actttgacct tgatatgctg + 1861 cctgctgacg ctcttgacga ttttgacctt gacatgctcc ccgggtcact aagtagcgcg + 1921 agacgaagac gaattctcta gatatcgctc aatactgacc atttaaatca tacctgacct + 1981 ccatagcaga aagtcaaaag cctccgaccg gaggcttttg acttgatcgg cacgtaagag + 2041 gttccaactt tcaccataat gaaataagat cactaccggg cgtatttttt gagttatcga + 2101 gattttcagg agctaaggaa gctaaaatga gccatattca acgggaaacg tcttgctcga + 2161 ggccgcgatt aaattccaac atggatgctg atttatatgg gtataaatgg gctcgcgata + 2221 atgtcgggca atcaggtgcg acaatctatc gattgtatgg gaagcccgat gcgccagagt + 2281 tgtttctgaa acatggcaaa ggtagcgttg ccaatgatgt tacagatgag atggtcaggc + 2341 taaactggct gacggaattt atgcctcttc cgaccatcaa gcattttatc cgtactcctg + 2401 atgatgcatg gttactcacc actgcgatcc cagggaaaac agcattccag gtattagaag + 2461 aatatcctga ttcaggtgaa aatattgttg atgcgctggc agtgttcctg cgccggttgc + 2521 attcgattcc tgtttgtaat tgtcctttta acggcgatcg cgtatttcgt ctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p1_5'-itr-pb.gb b/tools/create_assembly_picklists/test-data/emma_parts/p1_5'-itr-pb.gb new file mode 100644 index 00000000..15bf681d --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p1_5'-itr-pb.gb @@ -0,0 +1,78 @@ +LOCUS . 2163 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature complement(1174..1483) + /note="5'-ITR-PB" + source 1154..1503 + /source="Exported" + misc_feature complement(1509..1514) + /note="BsmBI" + terminator 1581..1612 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1613..1715 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1508..2163 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgt aggactatcc taacgtccac ttcttaaccc tagaaagata gtctgcgtaa + 1201 aattgacgca tgcattcttg aaatattgct ctctctttct aaatagcgcg aatccgtcgc + 1261 tgtgcattta ggacatctca gtcgccgctt ggagctcccg tgaggcgtgc ttgtcaatgc + 1321 ggtaagtgtc actgattttg aactataacg accgcgtgag tcaaaatgac gcatgattat + 1381 cttttacgtg acttttaaga tttaactcat acgataatta tattgttatt tcatgttcta + 1441 cttacgtgat aacttattat atatatattt tcttgttata gatcaggtgg atgaaagcgt + 1501 gtaatggcga gacgaagacg aattctctag atatcgctca atactgacca tttaaatcat + 1561 acctgacctc catagcagaa agtcaaaagc ctccgaccgg aggcttttga cttgatcggc + 1621 acgtaagagg ttccaacttt caccataatg aaataagatc actaccgggc gtattttttg + 1681 agttatcgag attttcagga gctaaggaag ctaaaatgag ccatattcaa cgggaaacgt + 1741 cttgctcgag gccgcgatta aattccaaca tggatgctga tttatatggg tataaatggg + 1801 ctcgcgataa tgtcgggcaa tcaggtgcga caatctatcg attgtatggg aagcccgatg + 1861 cgccagagtt gtttctgaaa catggcaaag gtagcgttgc caatgatgtt acagatgaga + 1921 tggtcaggct aaactggctg acggaattta tgcctcttcc gaccatcaag cattttatcc + 1981 gtactcctga tgatgcatgg ttactcacca ctgcgatccc agggaaaaca gcattccagg + 2041 tattagaaga atatcctgat tcaggtgaaa atattgttga tgcgctggca gtgttcctgc + 2101 gccggttgca ttcgattcct gtttgtaatt gtccttttaa cggcgatcgc gtatttcgtc + 2161 tcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p1_5'ha-haavs1.gb b/tools/create_assembly_picklists/test-data/emma_parts/p1_5'ha-haavs1.gb new file mode 100644 index 00000000..469ade3d --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p1_5'ha-haavs1.gb @@ -0,0 +1,87 @@ +LOCUS . 2723 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1154..2063 + /note="AVVS1-5'HA" + source 1154..2063 + /source="Exported" + misc_feature complement(2069..2074) + /note="BsmBI" + terminator 2141..2172 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 2173..2275 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 2068..2723 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgt agggcacctc tccatcctct tgctttcttt gcctggacac cccgttctcc + 1201 tgtggattcg ggtcacctct cactcctttc atttgggcag ctcccctacc ccccttacct + 1261 ctctagtctg tgctagctct tccagccccc tgtcatggca tcttccaggg gtccgagagc + 1321 tcagctagtc ttcttcctcc aacccgggcc cctatgtcca cttcaggaca gcatgtttgc + 1381 tgcctccagg gatcctgtgt ccccgagctg ggaccacctt atattcccag ggccggttaa + 1441 tgtggctctg gttctgggta cttttatctg tcccctccac cccacagtgg ggccactagg + 1501 gacaggattg gtgacagaaa agccccatcc ttaggcctcc tccttcctag tctcctgata + 1561 ttgggtctaa cccccacctc ctgttaggca gattccttat ctggtgacac acccccattt + 1621 cctggagcca tctctctcct tgccagaacc tctaaggttt gcttacgatg gagccagaga + 1681 ggatcctggg agggagagct tggcaggggg tgggagggaa gggggggatg cgtgacctgc + 1741 ccggttctca gtggccaccc tgcgctaccc tctcccagaa cctgagctgc tctgacgcgg + 1801 ctgtctggtg cgtttcactg atcctggtgc tgcagcttcc ttacacttcc caagaggaga + 1861 agcagtttgg aaaaacaaaa tcagaataag ttggtcctga gttctaactt tggctcttca + 1921 cctttctagt ccccaattta tattgttcct ccgtgcgtca gttttacctg tgagataagg + 1981 ccagtagcca gccccgtcct ggcagggctg tggtgaggag gggggtgtcc gtgtggaaaa + 2041 ctccctttgt gagaatggtg cgtatggcga gacgaagacg aattctctag atatcgctca + 2101 atactgacca tttaaatcat acctgacctc catagcagaa agtcaaaagc ctccgaccgg + 2161 aggcttttga cttgatcggc acgtaagagg ttccaacttt caccataatg aaataagatc + 2221 actaccgggc gtattttttg agttatcgag attttcagga gctaaggaag ctaaaatgag + 2281 ccatattcaa cgggaaacgt cttgctcgag gccgcgatta aattccaaca tggatgctga + 2341 tttatatggg tataaatggg ctcgcgataa tgtcgggcaa tcaggtgcga caatctatcg + 2401 attgtatggg aagcccgatg cgccagagtt gtttctgaaa catggcaaag gtagcgttgc + 2461 caatgatgtt acagatgaga tggtcaggct aaactggctg acggaattta tgcctcttcc + 2521 gaccatcaag cattttatcc gtactcctga tgatgcatgg ttactcacca ctgcgatccc + 2581 agggaaaaca gcattccagg tattagaaga atatcctgat tcaggtgaaa atattgttga + 2641 tgcgctggca gtgttcctgc gccggttgca ttcgattcct gtttgtaatt gtccttttaa + 2701 cggcgatcgc gtatttcgtc tcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p20_ct-minute-nes.gb b/tools/create_assembly_picklists/test-data/emma_parts/p20_ct-minute-nes.gb new file mode 100644 index 00000000..5370bcae --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p20_ct-minute-nes.gb @@ -0,0 +1,74 @@ +LOCUS . 1848 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + CDS 1156..1188 + /codon_start=1 + /note="minute NES" + /translation="MTKKFGTLTI" + source 1154..1188 + /source="Exported" + misc_feature complement(1194..1199) + /note="BsmBI" + terminator 1266..1297 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1298..1400 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1193..1848 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcga gcggaatgac caagaagttc ggcaccctga ccatctaatg gacgagacga + 1201 agacgaattc tctagatatc gctcaatact gaccatttaa atcatacctg acctccatag + 1261 cagaaagtca aaagcctccg accggaggct tttgacttga tcggcacgta agaggttcca + 1321 actttcacca taatgaaata agatcactac cgggcgtatt ttttgagtta tcgagatttt + 1381 caggagctaa ggaagctaaa atgagccata ttcaacggga aacgtcttgc tcgaggccgc + 1441 gattaaattc caacatggat gctgatttat atgggtataa atgggctcgc gataatgtcg + 1501 ggcaatcagg tgcgacaatc tatcgattgt atgggaagcc cgatgcgcca gagttgtttc + 1561 tgaaacatgg caaaggtagc gttgccaatg atgttacaga tgagatggtc aggctaaact + 1621 ggctgacgga atttatgcct cttccgacca tcaagcattt tatccgtact cctgatgatg + 1681 catggttact caccactgcg atcccaggga aaacagcatt ccaggtatta gaagaatatc + 1741 ctgattcagg tgaaaatatt gttgatgcgc tggcagtgtt cctgcgccgg ttgcattcga + 1801 ttcctgtttg taattgtcct tttaacggcg atcgcgtatt tcgtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p20_ct-nes.gb b/tools/create_assembly_picklists/test-data/emma_parts/p20_ct-nes.gb new file mode 100644 index 00000000..e9b3c175 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p20_ct-nes.gb @@ -0,0 +1,74 @@ +LOCUS . 1857 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + CDS 1156..1197 + /codon_start=1 + /note="NES" + /translation="ALALKLAGLDIGG" + source 1154..1197 + /source="Exported" + misc_feature complement(1203..1208) + /note="BsmBI" + terminator 1275..1306 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1307..1409 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1202..1857 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcga gcggagccct ggccctgaag ctggccggac tggacatcgg aggctaatgg + 1201 acgagacgaa gacgaattct ctagatatcg ctcaatactg accatttaaa tcatacctga + 1261 cctccatagc agaaagtcaa aagcctccga ccggaggctt ttgacttgat cggcacgtaa + 1321 gaggttccaa ctttcaccat aatgaaataa gatcactacc gggcgtattt tttgagttat + 1381 cgagattttc aggagctaag gaagctaaaa tgagccatat tcaacgggaa acgtcttgct + 1441 cgaggccgcg attaaattcc aacatggatg ctgatttata tgggtataaa tgggctcgcg + 1501 ataatgtcgg gcaatcaggt gcgacaatct atcgattgta tgggaagccc gatgcgccag + 1561 agttgtttct gaaacatggc aaaggtagcg ttgccaatga tgttacagat gagatggtca + 1621 ggctaaactg gctgacggaa tttatgcctc ttccgaccat caagcatttt atccgtactc + 1681 ctgatgatgc atggttactc accactgcga tcccagggaa aacagcattc caggtattag + 1741 aagaatatcc tgattcaggt gaaaatattg ttgatgcgct ggcagtgttc ctgcgccggt + 1801 tgcattcgat tcctgtttgt aattgtcctt ttaacggcga tcgcgtattt cgtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p20_linker3.gb b/tools/create_assembly_picklists/test-data/emma_parts/p20_linker3.gb new file mode 100644 index 00000000..b845765a --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p20_linker3.gb @@ -0,0 +1,74 @@ +LOCUS . 1850 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + CDS 1156..1188 + /codon_start=1 + /note="Linker 3" + /translation="GGGSGGGGSAS" + source 1154..1190 + /source="Exported" + misc_feature complement(1196..1201) + /note="BsmBI" + terminator 1268..1299 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1300..1402 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1195..1850 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcga gcggaggcgg aggaagcggc ggaggaggct cagccagcgc tggacgagac + 1201 gaagacgaat tctctagata tcgctcaata ctgaccattt aaatcatacc tgacctccat + 1261 agcagaaagt caaaagcctc cgaccggagg cttttgactt gatcggcacg taagaggttc + 1321 caactttcac cataatgaaa taagatcact accgggcgta ttttttgagt tatcgagatt + 1381 ttcaggagct aaggaagcta aaatgagcca tattcaacgg gaaacgtctt gctcgaggcc + 1441 gcgattaaat tccaacatgg atgctgattt atatgggtat aaatgggctc gcgataatgt + 1501 cgggcaatca ggtgcgacaa tctatcgatt gtatgggaag cccgatgcgc cagagttgtt + 1561 tctgaaacat ggcaaaggta gcgttgccaa tgatgttaca gatgagatgg tcaggctaaa + 1621 ctggctgacg gaatttatgc ctcttccgac catcaagcat tttatccgta ctcctgatga + 1681 tgcatggtta ctcaccactg cgatcccagg gaaaacagca ttccaggtat tagaagaata + 1741 tcctgattca ggtgaaaata ttgttgatgc gctggcagtg ttcctgcgcc ggttgcattc + 1801 gattcctgtt tgtaattgtc cttttaacgg cgatcgcgta tttcgtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p20_p2a.gb b/tools/create_assembly_picklists/test-data/emma_parts/p20_p2a.gb new file mode 100644 index 00000000..5c4e7f6c --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p20_p2a.gb @@ -0,0 +1,80 @@ +LOCUS . 1874 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + CDS 1156..1212 + /codon_start=1 + /note="P2A-Porcine teschovirus-1" + /note="Eukaryotic ribosomes fail to insert a peptide bond + between the Gly and Pro residues, yielding separate + polypeptides." + /product="2A peptide from porcine teschovirus-1 + polyprotein" + /translation="ATNFSLLKQAGDVEENPGP" + source 1154..1214 + /source="Exported" + misc_feature complement(1220..1225) + /note="BsmBI" + terminator 1292..1323 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1324..1426 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1219..1874 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcga gcggcgctac taacttcagc ctgctgaagc aggctggcga cgtggaggag + 1201 aaccctggac cttctggacg agacgaagac gaattctcta gatatcgctc aatactgacc + 1261 atttaaatca tacctgacct ccatagcaga aagtcaaaag cctccgaccg gaggcttttg + 1321 acttgatcgg cacgtaagag gttccaactt tcaccataat gaaataagat cactaccggg + 1381 cgtatttttt gagttatcga gattttcagg agctaaggaa gctaaaatga gccatattca + 1441 acgggaaacg tcttgctcga ggccgcgatt aaattccaac atggatgctg atttatatgg + 1501 gtataaatgg gctcgcgata atgtcgggca atcaggtgcg acaatctatc gattgtatgg + 1561 gaagcccgat gcgccagagt tgtttctgaa acatggcaaa ggtagcgttg ccaatgatgt + 1621 tacagatgag atggtcaggc taaactggct gacggaattt atgcctcttc cgaccatcaa + 1681 gcattttatc cgtactcctg atgatgcatg gttactcacc actgcgatcc cagggaaaac + 1741 agcattccag gtattagaag aatatcctga ttcaggtgaa aatattgttg atgcgctggc + 1801 agtgttcctg cgccggttgc attcgattcc tgtttgtaat tgtcctttta acggcgatcg + 1861 cgtatttcgt ctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p21_dmra.gb b/tools/create_assembly_picklists/test-data/emma_parts/p21_dmra.gb new file mode 100644 index 00000000..cc54ec20 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p21_dmra.gb @@ -0,0 +1,82 @@ +LOCUS . 2140 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + CDS 1814..2134 + /codon_start=1 + /note="FKBP (DmrA)" + /product="human FK506-binding protein FKBP12" + /translation="GVQVETISPGDGRTFPKRGQTCVVHYTGMLEDGKKFDSSRDRNKP + FKFMLGKQEVIRGWEEGVAQMSVGQRAKLTISPDYAYGATGHPGIIPPHATLVFDVELL + KLE" + source 1814..2140 + /source="Exported" +ORIGIN + 1 gttgcgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcgt ggaggagtgc aggtggaaac catctcccca ggcgacgggc gcaccttccc + 1861 caagcgcggc cagacctgcg tggtgcacta caccgggatg cttgaagatg gaaagaaatt + 1921 tgattcctcc cgggacagaa acaagccctt taagtttatg ctaggcaagc aggaggtgat + 1981 ccgaggctgg gaagaagggg ttgcccagat gagtgtgggt cagagagcca aactgactat + 2041 atctccagat tatgcctatg gtgccactgg gcacccaggc atcatcccac cacatgccac + 2101 tctcgtcttc gatgtggagc ttctaaaact ggaataataa +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p21_mkate2.gb b/tools/create_assembly_picklists/test-data/emma_parts/p21_mkate2.gb new file mode 100644 index 00000000..77d13bb4 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p21_mkate2.gb @@ -0,0 +1,90 @@ +LOCUS . 2509 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + CDS 1814..2506 + /codon_start=1 + /gene="mKate2" + /note="mKate2" + /translation="VSELIKENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMRIKA + VEGGPLPFAFDILATSFMYGSKTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGVLTA + TQDTSLQDGCLIYNVKIRGVNFPSNGPVMQKKTLGWEASTETLYPADGGLEGRADMALK + LVGGGHLICNLKTTYRSKKPAKNLKMPGVYYVDRRLERIKEADKETYVEQHEVAVARYC + DLPSKLGHR" + source 1814..2509 + /source="Exported" +ORIGIN + 1 gttgcgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcgt ggagtgagcg agctgattaa ggagaacatg cacatgaagc tgtacatgga + 1861 gggcaccgtg aacaaccacc acttcaagtg cacatccgag ggcgaaggca agccctacga + 1921 gggcacccag accatgagaa tcaaggcggt cgagggcggc cctctcccct tcgccttcga + 1981 catcctggct accagcttca tgtacggcag caaaaccttc atcaaccaca cccagggcat + 2041 ccccgacttc tttaagcagt ccttccccga gggcttcaca tgggagagag tcaccacata + 2101 cgaagacggg ggcgtgctga ccgctaccca ggacaccagc ctccaggacg gctgcctcat + 2161 ctacaacgtc aagatcagag gggtgaactt cccatccaac ggccctgtga tgcagaagaa + 2221 aacactcggc tgggaggcct ccaccgaaac cctgtacccc gctgacggcg gcctggaagg + 2281 cagagccgac atggccctga agctcgtggg cgggggccac ctgatctgca acttgaagac + 2341 cacatacaga tccaagaaac ccgctaagaa cctcaagatg cccggcgtct actatgtgga + 2401 cagaagactg gaaagaatca aggaggccga caaagaaacc tacgtcgagc agcacgaggt + 2461 ggctgtggcc agatactgcg acctccctag caaactgggg cacagataa +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p21_mneogreen.gb b/tools/create_assembly_picklists/test-data/emma_parts/p21_mneogreen.gb new file mode 100644 index 00000000..8d680fb7 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p21_mneogreen.gb @@ -0,0 +1,92 @@ +LOCUS . 2521 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + CDS 1814..2518 + /codon_start=1 + /note="mNeonGreen" + /product="bright monomeric yellow-green fluorescent protein + derived from LanYFP (Shaner et al., 2013)" + /translation="VSKGEEDNMASLPATHELHIFGSINGVDFDMVGQGTGNPNDGYEE + LNLKSTKGDLQFSPWILVPHIGYGFHQYLPYPDGMSPFQAAMVDGSGYQVHRTMQFEDG + ASLTVNYRYTYEGSHIKGEAQVKGTGFPADGPVMTNSLTAADWCRSKKTYPNDKTIIST + FKWSYTTGNGKRYRSTARTTYTFAKPMAANYLKNQPMYVFRKTELKHSKTELNFKEWQK + AFTDVMGMDELYK" + source 1814..2521 + /source="Exported" +ORIGIN + 1 gttgcgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcgt ggagtgagca agggcgagga ggataacatg gcctctctcc cagcgacaca + 1861 tgagttacac atctttggct ccatcaacgg tgtggacttt gacatggtgg gtcagggcac + 1921 cggcaatcca aatgatggtt atgaggagtt aaacctgaag tccaccaagg gtgacctcca + 1981 gttctccccc tggattctgg tccctcatat cgggtatggc ttccatcagt acctgcccta + 2041 ccctgacggg atgtcgcctt tccaggccgc catggtagat ggctccggat accaagtcca + 2101 tcgcacaatg cagtttgaag atggtgcctc ccttactgtt aactaccgct acacctacga + 2161 gggaagccac atcaaaggag aggcccaggt gaaggggact ggtttccctg ctgacggtcc + 2221 tgtgatgacc aactcgctga ccgctgcgga ctggtgcagg tcgaagaaga cttaccccaa + 2281 cgacaaaacc atcatcagta cctttaagtg gagttacacc actggaaatg gcaagcgcta + 2341 ccggagcact gcgcggacca cctacacctt tgccaagcca atggcggcta actatctgaa + 2401 gaaccagccg atgtacgtgt tccgtaagac ggagctcaag cactccaaga ccgagctcaa + 2461 cttcaaggag tggcaaaagg cctttaccga tgtgatgggc atggacgagc tgtacaagta + 2521 a +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p21_mruby2.gb b/tools/create_assembly_picklists/test-data/emma_parts/p21_mruby2.gb new file mode 100644 index 00000000..f65260a6 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p21_mruby2.gb @@ -0,0 +1,93 @@ +LOCUS . 2524 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + CDS 1814..2521 + /codon_start=1 + /note="mRuby2" + /product="monomeric red fluorescent protein derived from + mRuby, with improved photophysical properties (Lam et al., + 2012)" + /translation="VSKGEELIKENMRMKVVMEGSVNGHQFKCTGEGEGNPYMGTQTMR + IKVIEGGPLPFAFDILATSFMYGSRTFIKYPKGIPDFFKQSFPEGFTWERVTRYEDGGV + VTVMQDTSLEDGCLVYHVQVRGVNFPSNGPVMQKKTKGWEPNTEMMYPADGGLRGYTHM + ALKVDGGGHLSCSFVTTYRSKKTVGNIKMPGIHAVDHRLERLEESDNEMFVVQREHAVA + KFAGLGGGMDELYK" + source 1814..2524 + /source="Exported" +ORIGIN + 1 gttgcgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcgt ggagtgtcta agggcgaaga gctgatcaag gaaaatatgc gtatgaaggt + 1861 ggtcatggaa ggttcggtca acggccacca attcaaatgc acaggtgaag gagaaggcaa + 1921 tccgtacatg ggaactcaaa ccatgaggat caaagtcatc gagggaggac ccctgccatt + 1981 tgcctttgac attcttgcca cgtcgttcat gtatggcagc cgtactttta tcaagtaccc + 2041 gaaaggcatt cctgatttct ttaaacagtc ctttcctgag ggttttactt gggaaagagt + 2101 tacgagatac gaagatggtg gagtcgtcac cgtcatgcag gacaccagcc ttgaggatgg + 2161 ctgtctcgtt taccacgtcc aagtcagagg ggtaaacttt ccctccaatg gtcccgtgat + 2221 gcagaagaag accaagggtt gggagcctaa tacagagatg atgtatccag cagatggtgg + 2281 tctgagggga tacactcata tggcactgaa agttgatggt ggtggccatc tgtcttgctc + 2341 tttcgtaaca acttacaggt caaaaaagac cgtcgggaac atcaagatgc ccggtatcca + 2401 tgccgttgat caccgcctgg aaaggttaga ggaaagtgac aatgaaatgt tcgtagtaca + 2461 acgcgaacac gcagttgcca agttcgccgg gcttggtggt gggatggacg agctgtacaa + 2521 gtaa +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p21_mtagbfp2.gb b/tools/create_assembly_picklists/test-data/emma_parts/p21_mtagbfp2.gb new file mode 100644 index 00000000..1661e877 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p21_mtagbfp2.gb @@ -0,0 +1,93 @@ +LOCUS . 2524 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + CDS 1814..2521 + /codon_start=1 + /note="mTagBFP2" + /note="mammalian codon-optimized" + /product="enhanced monomeric blue fluorescent protein + (Subach et al., 2011)" + /translation="VSKGEELIKENMHMKLYMEGTVDNHHFKCTSEGEGKPYEGTQTMR + IKVVEGGPLPFAFDILATSFLYGSKTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGV + LTATQDTSLQDGCLIYNVKIRGVNFTSNGPVMQKKTLGWEAFTETLYPADGGLEGRNDM + ALKLVGGSHLIANAKTTYRSKKPAKNLKMPGVYYVDYRLERIKEANNETYVEQHEVAVA + RYCDLPSKLGHKLN" + source 1814..2524 + /source="Exported" +ORIGIN + 1 gttgcgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcgt ggagtgtcta agggcgaaga gctgattaag gagaacatgc acatgaagct + 1861 gtacatggag ggcaccgtgg acaaccatca cttcaagtgc acatccgagg gcgaaggcaa + 1921 gccctacgag ggcacccaga ccatgagaat caaggtggtc gagggcggcc ctctcccctt + 1981 cgccttcgac atcctggcta ctagcttcct ctacggcagc aagaccttca tcaaccacac + 2041 ccagggcatc cccgacttct tcaagcagtc cttccctgag ggcttcacat gggagagagt + 2101 caccacatac gaagacgggg gcgtgctgac cgctacccag gacaccagcc tccaggacgg + 2161 ctgcctcatc tacaacgtca agatcagagg ggtgaacttc acatccaacg gccctgtgat + 2221 gcagaagaaa acactcggct gggaggcctt caccgaaacg ctgtaccccg ctgacggcgg + 2281 cctggaaggc agaaacgaca tggccctgaa gctcgtgggc gggagccatc tgatcgcaaa + 2341 cgccaagacc acatatagat ccaagaaacc cgctaagaac ctcaagatgc ctggcgtcta + 2401 ctatgtggac tacagactgg aaagaatcaa ggaggccaac aacgaaacct acgtcgagca + 2461 gcacgaggtg gcagtggcca gatactgcga cctccctagc aaactggggc acaagcttaa + 2521 ttaa +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p21_puror.gb b/tools/create_assembly_picklists/test-data/emma_parts/p21_puror.gb new file mode 100644 index 00000000..1d7c5f81 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p21_puror.gb @@ -0,0 +1,90 @@ +LOCUS . 2413 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + CDS 1814..2410 + /codon_start=1 + /gene="pac from Streptomyces" + /note="PuroR" + /note="confers resistance to puromycin" + /product="puromycin N-acetyltransferase" + /translation="TEYKPTVRLATRDDVPRAVRTLAAAFADYPATRHTVDPDRHIERV + TELQELFLTRVGLDIGKVWVADDGAAVAVWTTPESVEAGAVFAEIGPRMAELSGSRLAA + QQQMEGLLAPHRPKEPAWFLATVGVSPDHQGKGLGSAVVLPGVEAAERAGVPAFLETSA + PRNLPFYERLGFTVTADVECPKDRATWCMTRKPGA" + source 1814..2413 + /source="Exported" +ORIGIN + 1 gttgcgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcgt ggaaccgagt acaagcccac ggtgcgcctc gccacccgcg acgacgtccc + 1861 cagggccgta cgcaccctcg ccgccgcgtt cgccgactac cccgccacgc gccacaccgt + 1921 cgatccggac cgccacatcg agcgggtcac cgagctgcaa gaactcttcc tcacgcgcgt + 1981 cgggctcgac atcggcaagg tgtgggtcgc ggacgacggc gccgcggtgg cggtctggac + 2041 cacgccggag agcgtcgaag cgggggcggt gttcgccgag atcggcccgc gcatggccga + 2101 gttgagcggt tcccggctgg ccgcgcagca acagatggaa ggcctcctgg cgccgcaccg + 2161 gcccaaggag cccgcgtggt tcctggccac cgtcggcgtg tcgcccgacc accagggcaa + 2221 gggtctgggc agcgccgtcg tgctccccgg agtggaggcg gccgagcgcg ccggggtgcc + 2281 cgccttcctg gaaacctccg cgccccgcaa cctccccttc tacgagcggc tcggcttcac + 2341 cgtcaccgcc gacgtcgagt gcccgaagga ccgcgcgacc tggtgcatga cccgcaagcc + 2401 cggtgcctaa taa +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p22_pgkpolya.gb b/tools/create_assembly_picklists/test-data/emma_parts/p22_pgkpolya.gb new file mode 100644 index 00000000..f61c9942 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p22_pgkpolya.gb @@ -0,0 +1,76 @@ +LOCUS . 2042 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + polyA_signal 1837..2042 + /note="PGK-polyA" + source 1814..2042 + /source="Exported" +ORIGIN + 1 cgaacgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcgg ttgccttgag catctgactt ctggctaaat tgatgatcta ttaaacaata + 1861 aagatgtcca catggaagtt ttttcctgtc atactttgtt aagaagggtg agaacagagt + 1921 acctacattt tgaatggaag gattggagct acgggggtgg gggtggggtg ggattagata + 1981 aatgcctgct ctttactgaa ggctctttac tattgcttta tgataatgtt tcatagttgg + 2041 at +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p23_insulatorfb.gb b/tools/create_assembly_picklists/test-data/emma_parts/p23_insulatorfb.gb new file mode 100644 index 00000000..659c48aa --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p23_insulatorfb.gb @@ -0,0 +1,74 @@ +LOCUS . 1954 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + misc_feature 1814..1954 + /note="Insulator FB-pos23" + source 1814..1954 + /source="Exported" +ORIGIN + 1 cacgcgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcgc gaaggccgcg aattctgaaa gaccccacct gtaggtttgg caagcccagg + 1861 gatgtacgtc cctaacccgc tagggggcag caactagtcc caggcctgca ctgccgcctg + 1921 ccggcagggg tccagtcgct agcgcatgcc tgca +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p24_3'ha_haavs1.gb b/tools/create_assembly_picklists/test-data/emma_parts/p24_3'ha_haavs1.gb new file mode 100644 index 00000000..e7563f86 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p24_3'ha_haavs1.gb @@ -0,0 +1,82 @@ +LOCUS . 2446 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + misc_feature 1814..2446 + /note="3'-HA_hAAVS1" + source 1814..2446 + /source="Exported" +ORIGIN + 1 actgcgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcgc acgccgcctc tactcccttt ctctttctcc atccttcttt ccttaaagag + 1861 tccccagtgc tatctgggac atattcctcc gcccagagca gggtcccgct tccctaaggc + 1921 cctgctctgg gcttctgggt ttgagtcctt ggcaagccca ggagaggcgc tcaggcttcc + 1981 ctgtccccct tcctcgtcca ccatctcatg cccctggctc tcctgcccct tccctacagg + 2041 ggttcctggc tctgctcttc agactgagcc ccgttcccct gcatccccgt tcccctgcat + 2101 cccccttccc ctgcatcccc cagaggcccc aggccaccta cttggcctgg accccacgag + 2161 aggccacccc agccctgtct accaggctgc cttttgggtg gattctcctc caactgtggg + 2221 gtgactgctt ggcaaactca ctcttcgggg tatcccagga ggcctggagc attggggtgg + 2281 gctggggttc agagaggagg gattcccttc tcaggttacg tggccaagaa gcaggggagc + 2341 tgggtttggg tcaggtctgg gtgtggggtg accagcttat gctgtttgcc caggacagcc + 2401 tagttttagc actgaaaccc tcagtctaat ggttacaaat aaagca +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p24_3'pb.gb b/tools/create_assembly_picklists/test-data/emma_parts/p24_3'pb.gb new file mode 100644 index 00000000..b87d1d9d --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p24_3'pb.gb @@ -0,0 +1,76 @@ +LOCUS . 2060 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + misc_feature complement(1834..2039) + /note="Piggy 3'" + source 1814..2060 + /source="Exported" +ORIGIN + 1 actgcgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcgc acgtgcatcc acgatctagt cactttgtta ctttatagaa gaaattttga + 1861 gtttttgttt ttttttaata aataaataaa cataaataaa ttgtttgttg aatttattat + 1921 tagtatgtaa gtgtaaatat aataaaactt aatatctatt caaattaata aataaacgtc + 1981 aattttacgc atgattatct ttaacgtacg tcacaatatg attatctttc tagggttaac + 2041 tactcaccct cgagcataac +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p25_sv40-ori.gb b/tools/create_assembly_picklists/test-data/emma_parts/p25_sv40-ori.gb new file mode 100644 index 00000000..17470dab --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p25_sv40-ori.gb @@ -0,0 +1,75 @@ +LOCUS . 1949 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + rep_origin 1814..1949 + /note="SV40-ORI" + /note="SV40 origin of replication" + source 1814..1949 + /source="Exported" +ORIGIN + 1 acgacgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcga ctgatcccgc ccctaactcc gcccagttcc gcccattctc cgccccatgg + 1861 ctgactaatt ttttttattt atgcagaggc cgaggccgcc tctgcctctg agctattcca + 1921 gaagtagtga ggaggctttt ttggaggcc +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p2_insulatorfb.gb b/tools/create_assembly_picklists/test-data/emma_parts/p2_insulatorfb.gb new file mode 100644 index 00000000..a6dfb999 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p2_insulatorfb.gb @@ -0,0 +1,74 @@ +LOCUS . 1954 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1154..1294 + /note="Insulator FB" + source 1154..1294 + /source="Exported" + misc_feature complement(1300..1305) + /note="BsmBI" + terminator 1372..1403 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1404..1506 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1299..1954 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcga tggggccgcg aattctgaaa gaccccacct gtaggtttgg caagcccagg + 1201 gatgtacgtc cctaacccgc tagggggcag caactagtcc caggcctgca ctgccgcctg + 1261 ccggcagggg tccagtcgct agcgcatgcc tgcagactcg agacgaagac gaattctcta + 1321 gatatcgctc aatactgacc atttaaatca tacctgacct ccatagcaga aagtcaaaag + 1381 cctccgaccg gaggcttttg acttgatcgg cacgtaagag gttccaactt tcaccataat + 1441 gaaataagat cactaccggg cgtatttttt gagttatcga gattttcagg agctaaggaa + 1501 gctaaaatga gccatattca acgggaaacg tcttgctcga ggccgcgatt aaattccaac + 1561 atggatgctg atttatatgg gtataaatgg gctcgcgata atgtcgggca atcaggtgcg + 1621 acaatctatc gattgtatgg gaagcccgat gcgccagagt tgtttctgaa acatggcaaa + 1681 ggtagcgttg ccaatgatgt tacagatgag atggtcaggc taaactggct gacggaattt + 1741 atgcctcttc cgaccatcaa gcattttatc cgtactcctg atgatgcatg gttactcacc + 1801 actgcgatcc cagggaaaac agcattccag gtattagaag aatatcctga ttcaggtgaa + 1861 aatattgttg atgcgctggc agtgttcctg cgccggttgc attcgattcc tgtttgtaat + 1921 tgtcctttta acggcgatcg cgtatttcgt ctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p3_cagp.gb b/tools/create_assembly_picklists/test-data/emma_parts/p3_cagp.gb new file mode 100644 index 00000000..9f0eab38 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p3_cagp.gb @@ -0,0 +1,86 @@ +LOCUS . 2503 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + enhancer 1172..1551 + /note="CMV enhancer" + /note="human cytomegalovirus immediate early enhancer" + promoter 1553..1828 + /note="chicken beta-actin promoter" + source 1154..1843 + /source="Exported" + misc_feature complement(1849..1854) + /note="BsmBI" + terminator 1921..1952 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1953..2055 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1848..2503 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgg actggatctg atatcatcgt cgacattgat tattgactag ttattaatag + 1201 taatcaatta cggggtcatt agttcatagc ccatatatgg agttccgcgt tacataactt + 1261 acggtaaatg gcccgcctgg ctgaccgccc aacgaccccc gcccattgac gtcaataatg + 1321 acgtatgttc ccatagtaac gccaataggg actttccatt gacgtcaatg ggtggactat + 1381 ttacggtaaa ctgcccactt ggcagtacat caagtgtatc atatgccaag tacgccccct + 1441 attgacgtca atgacggtaa atggcccgcc tggcattatg cccagtacat gaccttatgg + 1501 gactttccta cttggcagta catctacgta ttagtcatcg ctattaccat ggtcgaggtg + 1561 agccccacgt tctgcttcac tctccccatc tcccccccct ccccaccccc aattttgtat + 1621 ttatttattt tttaattatt ttgtgcagcg atgggggcgg gggggggggg ggcgcgcgcc + 1681 aggcggggcg gggcggggcg aggggcgggg cggggcgagg cggagaggtg cggcggcagc + 1741 caatcagagc ggcgcgctcc gaaagtttcc ttttatggcg aggcggcggc ggcggcggcc + 1801 ctataaaaag cgaagcgcgc ggcgggcggg agtcgctgcg ttgggaccga gacgaagacg + 1861 aattctctag atatcgctca atactgacca tttaaatcat acctgacctc catagcagaa + 1921 agtcaaaagc ctccgaccgg aggcttttga cttgatcggc acgtaagagg ttccaacttt + 1981 caccataatg aaataagatc actaccgggc gtattttttg agttatcgag attttcagga + 2041 gctaaggaag ctaaaatgag ccatattcaa cgggaaacgt cttgctcgag gccgcgatta + 2101 aattccaaca tggatgctga tttatatggg tataaatggg ctcgcgataa tgtcgggcaa + 2161 tcaggtgcga caatctatcg attgtatggg aagcccgatg cgccagagtt gtttctgaaa + 2221 catggcaaag gtagcgttgc caatgatgtt acagatgaga tggtcaggct aaactggctg + 2281 acggaattta tgcctcttcc gaccatcaag cattttatcc gtactcctga tgatgcatgg + 2341 ttactcacca ctgcgatccc agggaaaaca gcattccagg tattagaaga atatcctgat + 2401 tcaggtgaaa atattgttga tgcgctggca gtgttcctgc gccggttgca ttcgattcct + 2461 gtttgtaatt gtccttttaa cggcgatcgc gtatttcgtc tcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p3_cmvp_tet.gb b/tools/create_assembly_picklists/test-data/emma_parts/p3_cmvp_tet.gb new file mode 100644 index 00000000..b7bd9c1a --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p3_cmvp_tet.gb @@ -0,0 +1,98 @@ +LOCUS . 2440 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + enhancer 1154..1533 + /note="CMV enhancer" + /note="human cytomegalovirus immediate early enhancer" + promoter 1534..1737 + /note="CMV promoter" + /note="human cytomegalovirus (CMV) immediate early + promoter" + TATA_signal 1723..1729 + protein_bind 1739..1757 + /bound_moiety="tetracycline repressor TetR" + /gene="tetO" + /note="tet operator" + /note="bacterial operator O2 for the tetR and tetA genes" + protein_bind 1760..1778 + /bound_moiety="tetracycline repressor TetR" + /gene="tetO" + /note="tet operator" + /note="bacterial operator O2 for the tetR and tetA genes" + source 1154..1780 + /source="Exported" + misc_feature complement(1786..1791) + /note="BsmBI" + terminator 1858..1889 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1890..1992 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1785..2440 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgg actgacattg attattgact agttattaat agtaatcaat tacggggtca + 1201 ttagttcata gcccatatat ggagttccgc gttacataac ttacggtaaa tggcccgcct + 1261 ggctgaccgc ccaacgaccc ccgcccattg acgtcaataa tgacgtatgt tcccatagta + 1321 acgccaatag ggactttcca ttgacgtcaa tgggtggagt atttacggta aactgcccac + 1381 ttggcagtac atcaagtgta tcatatgcca agtacgcccc ctattgacgt caatgacggt + 1441 aaatggcccg cctggcatta tgcccagtac atgaccttat gggactttcc tacttggcag + 1501 tacatctacg tattagtcat cgctattacc atggtgatgc ggttttggca gtacatcaat + 1561 gggcgtggat agcggtttga ctcacgggga tttccaagtc tccaccccat tgacgtcaat + 1621 gggagtttgt tttggaacca aaatcaacgg gactttccaa aatgtcgtaa caactccgcc + 1681 ccattgacgc aaatgggcgg taggcgtgta cggtgggagg tctatataag cagagctctc + 1741 cctatcagtg atagagatct ccctatcagt gatagagatt ggaccgagac gaagacgaat + 1801 tctctagata tcgctcaata ctgaccattt aaatcatacc tgacctccat agcagaaagt + 1861 caaaagcctc cgaccggagg cttttgactt gatcggcacg taagaggttc caactttcac + 1921 cataatgaaa taagatcact accgggcgta ttttttgagt tatcgagatt ttcaggagct + 1981 aaggaagcta aaatgagcca tattcaacgg gaaacgtctt gctcgaggcc gcgattaaat + 2041 tccaacatgg atgctgattt atatgggtat aaatgggctc gcgataatgt cgggcaatca + 2101 ggtgcgacaa tctatcgatt gtatgggaag cccgatgcgc cagagttgtt tctgaaacat + 2161 ggcaaaggta gcgttgccaa tgatgttaca gatgagatgg tcaggctaaa ctggctgacg + 2221 gaatttatgc ctcttccgac catcaagcat tttatccgta ctcctgatga tgcatggtta + 2281 ctcaccactg cgatcccagg gaaaacagca ttccaggtat tagaagaata tcctgattca + 2341 ggtgaaaata ttgttgatgc gctggcagtg ttcctgcgcc ggttgcattc gattcctgtt + 2401 tgtaattgtc cttttaacgg cgatcgcgta tttcgtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p3_ef1ap.gb b/tools/create_assembly_picklists/test-data/emma_parts/p3_ef1ap.gb new file mode 100644 index 00000000..bd2339d6 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p3_ef1ap.gb @@ -0,0 +1,98 @@ +LOCUS . 3037 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + promoter 5..1183 + /note="EF-1-alpha promoter" + /note="strong constitutive promoter for human elongation + factor EF-1-alpha" + intron 236..1174 + /note="EF-1-alpha intron A" + /note="intron upstream of the start codon of human + EF-1-alpha" + source 5..1228 + /source="Exported" + misc_feature complement(1234..1239) + /note="BsmBI" + terminator 1306..1337 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1338..1440 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1233..1888 + /source="Exported" + terminator 2280..2307 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(2319..2906) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 2928..2957 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 3031..3036 + /note="BsmBI" + source 1893..3037 + /source="Exported" +ORIGIN + 1 gactggctcc ggtgcccgtc agtgggcaga gcgcacatcg cccacagtcc ccgagaagtt + 61 ggggggaggg gtcggcaatt gaaccggtgc ctagagaagg tggcgcgggg taaactggga + 121 aagtgatgtc gtgtactggc tccgcctttt tcccgagggt gggggagaac cgtatataag + 181 tgcagtagtc gccgtgaacg ttctttttcg caacgggttt gccgccagaa cacaggtaag + 241 tgccgtgtgt ggttcccgcg ggcctggcct ctttacgggt tatggccctt gcgtgccttg + 301 aattacttcc acctggctgc agtacgtgat tcttgatccc gagcttcggg ttggaagtgg + 361 gtgggagagt tcgaggcctt gcgcttaagg agccccttcg cctcgtgctt gagttgaggc + 421 ctggcctggg cgctggggcc gccgcgtgcg aatctggtgg caccttcgcg cctgtctcgc + 481 tgctttcgat aagtctctag ccatttaaaa tttttgatga cctgctgcga cgcttttttt + 541 ctggcaagat agtcttgtaa atgcgggcca agatctgcac actggtattt cggtttttgg + 601 ggccgcgggc ggcgacgggg cccgtgcgtc ccagcgcaca tgttcggcga ggcggggcct + 661 gcgagcgcgg ccaccgagaa tcggacgggg gtagtctcaa gctggccggc ctgctctggt + 721 gcctggcctc gcgccgccgt gtatcgcccc gccctgggcg gcaaggctgg cccggtcggc + 781 accagttgcg tgagcggaaa gatggccgct tcccggccct gctgcaggga gctcaaaatg + 841 gaggacgcgg cgctcgggag agcgggcggg tgagtcaccc acacaaagga aaagggcctt + 901 tccgtcctca gccgtcgctt catgtgactc cacggagtac cgggcgccgt ccaggcacct + 961 cgattagttc tcgagctttt ggagtacgtc gtctttaggt tggggggagg ggttttatgc + 1021 gatggagttt ccccacactg agtgggtgga gactgaagtt aggccagctt ggcacttgat + 1081 gtaattctcc ttggaatttg ccctttttga gtttggatct tggttcattc tcaagcctca + 1141 gacagtggtt caaagttttt ttcttccatt tcaggtgtcg tgacgctagc gctaccggac + 1201 tcagatctcg agctcaagct tcgaattcgg accgagacga agacgaattc tctagatatc + 1261 gctcaatact gaccatttaa atcatacctg acctccatag cagaaagtca aaagcctccg + 1321 accggaggct tttgacttga tcggcacgta agaggttcca actttcacca taatgaaata + 1381 agatcactac cgggcgtatt ttttgagtta tcgagatttt caggagctaa ggaagctaaa + 1441 atgagccata ttcaacggga aacgtcttgc tcgaggccgc gattaaattc caacatggat + 1501 gctgatttat atgggtataa atgggctcgc gataatgtcg ggcaatcagg tgcgacaatc + 1561 tatcgattgt atgggaagcc cgatgcgcca gagttgtttc tgaaacatgg caaaggtagc + 1621 gttgccaatg atgttacaga tgagatggtc aggctaaact ggctgacgga atttatgcct + 1681 cttccgacca tcaagcattt tatccgtact cctgatgatg catggttact caccactgcg + 1741 atcccaggga aaacagcatt ccaggtatta gaagaatatc ctgattcagg tgaaaatatt + 1801 gttgatgcgc tggcagtgtt cctgcgccgg ttgcattcga ttcctgtttg taattgtcct + 1861 tttaacggcg atcgcgtatt tcgtctcgct caggcgcaat cacgaatgaa taacggtttg + 1921 gttggtgcga gtgattttga tgacgagcgt aatggctggc ctgttgaaca agtctggaaa + 1981 gaaatgcata agcttttgcc attctcaccg gattcagtcg tcactcatgg tgatttctca + 2041 cttgataacc ttatttttga cgaggggaaa ttaataggtt gtattgatgt tggacgagtc + 2101 ggaatcgcag accgatacca ggatcttgcc atcctatgga actgcctcgg tgagttttct + 2161 ccttcattac agaaacggct ttttcaaaaa tatggtattg ataatcctga tatgaataaa + 2221 ttgcagtttc acttgatgct cgatgagttt ttctaatgag ggcccaaatg taatcacctg + 2281 gctcaccttc gggtgggcct ttctgcgttg ctggcgtttt tccataggct ccgcccccct + 2341 gacgagcatc acaaaaatcg atgctcaagt cagaggtggc gaaacccgac aggactataa + 2401 agataccagg cgtttccccc tggaagctcc ctcgtgcgct ctcctgttcc gaccctgccg + 2461 cttaccggat acctgtccgc ctttctccct tcgggaagcg tggcgctttc tcatagctca + 2521 cgctgtaggt atctcagttc ggtgtaggtc gttcgctcca agctgggctg tgtgcacgaa + 2581 ccccccgttc agcccgaccg ctgcgcctta tccggtaact atcgtcttga gtccaacccg + 2641 gtaagacacg acttatcgcc actggcagca gccactggta acaggattag cagagcgagg + 2701 tatgtaggcg gtgctacaga gttcttgaag tggtggccta actacggcta cactagaaga + 2761 acagtatttg gtatctgcgc tctgctgaag ccagttacct cggaaaaaga gttggtagct + 2821 cttgatccgg caaacaaacc accgctggta gcggtggttt ttttgtttgc aagcagcaga + 2881 ttacgcgcag aaaaaaagga tctcaagaag atcctttgat tttctaccga agaaaggccc + 2941 acccgtgaag gtgagccagt gagttgattg cagtccagtt acgctggagt ctgaggctcg + 3001 tcctgaatga tatcaagctt gaattcgtta cgtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p3_tre3gp.gb b/tools/create_assembly_picklists/test-data/emma_parts/p3_tre3gp.gb new file mode 100644 index 00000000..e19195f0 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p3_tre3gp.gb @@ -0,0 +1,115 @@ +LOCUS . 2209 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + promoter 1171..1549 + /note="TRE3G promoter" + /note="3rd-generation Tet-responsive promoter that can be + activated by binding of Tet-On(R) 3G" + protein_bind 1179..1197 + /bound_moiety="tetracycline repressor TetR" + /gene="tetO" + /note="tet operator" + /note="bacterial operator O2 for the tetR and tetA genes" + protein_bind 1215..1233 + /bound_moiety="tetracycline repressor TetR" + /gene="tetO" + /note="tet operator" + /note="bacterial operator O2 for the tetR and tetA genes" + protein_bind 1251..1269 + /bound_moiety="tetracycline repressor TetR" + /gene="tetO" + /note="tet operator" + /note="bacterial operator O2 for the tetR and tetA genes" + protein_bind 1287..1305 + /bound_moiety="tetracycline repressor TetR" + /gene="tetO" + /note="tet operator" + /note="bacterial operator O2 for the tetR and tetA genes" + protein_bind 1323..1341 + /bound_moiety="tetracycline repressor TetR" + /gene="tetO" + /note="tet operator" + /note="bacterial operator O2 for the tetR and tetA genes" + protein_bind 1359..1377 + /bound_moiety="tetracycline repressor TetR" + /gene="tetO" + /note="tet operator" + /note="bacterial operator O2 for the tetR and tetA genes" + protein_bind 1395..1413 + /bound_moiety="tetracycline repressor TetR" + /gene="tetO" + /note="tet operator" + /note="bacterial operator O2 for the tetR and tetA genes" + source 1154..1549 + /source="Exported" + misc_feature complement(1555..1560) + /note="BsmBI" + terminator 1627..1658 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1659..1761 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1554..2209 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgg actttatacg aagttatctc gagtttactc cctatcagtg atagagaacg + 1201 tatgaagagt ttactcccta tcagtgatag agaacgtatg cagactttac tccctatcag + 1261 tgatagagaa cgtataagga gtttactccc tatcagtgat agagaacgta tgaccagttt + 1321 actccctatc agtgatagag aacgtatcta cagtttactc cctatcagtg atagagaacg + 1381 tatatccagt ttactcccta tcagtgatag agaacgtata agctttaggc gtgtacggtg + 1441 ggcgcctata aaagcagagc tcgtttagtg aaccgtcaga tcgcctggag caattccaca + 1501 acacttttgt cttataccaa ctttccgtac cacttcctac cctcgtaaag gaccgagacg + 1561 aagacgaatt ctctagatat cgctcaatac tgaccattta aatcatacct gacctccata + 1621 gcagaaagtc aaaagcctcc gaccggaggc ttttgacttg atcggcacgt aagaggttcc + 1681 aactttcacc ataatgaaat aagatcacta ccgggcgtat tttttgagtt atcgagattt + 1741 tcaggagcta aggaagctaa aatgagccat attcaacggg aaacgtcttg ctcgaggccg + 1801 cgattaaatt ccaacatgga tgctgattta tatgggtata aatgggctcg cgataatgtc + 1861 gggcaatcag gtgcgacaat ctatcgattg tatgggaagc ccgatgcgcc agagttgttt + 1921 ctgaaacatg gcaaaggtag cgttgccaat gatgttacag atgagatggt caggctaaac + 1981 tggctgacgg aatttatgcc tcttccgacc atcaagcatt ttatccgtac tcctgatgat + 2041 gcatggttac tcaccactgc gatcccaggg aaaacagcat tccaggtatt agaagaatat + 2101 cctgattcag gtgaaaatat tgttgatgcg ctggcagtgt tcctgcgccg gttgcattcg + 2161 attcctgttt gtaattgtcc ttttaacggc gatcgcgtat ttcgtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p4_kt-l7ae -weiss.gb b/tools/create_assembly_picklists/test-data/emma_parts/p4_kt-l7ae -weiss.gb new file mode 100644 index 00000000..965dd078 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p4_kt-l7ae -weiss.gb @@ -0,0 +1,72 @@ +LOCUS . 1845 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1156..1182 + /note="Kt - L7Ae" + source 1154..1185 + /source="Exported" + misc_feature complement(1191..1196) + /note="BsmBI" + terminator 1263..1294 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1295..1397 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1190..1845 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgg gacaaggatc cgtgatcgga aacgtgagat ccagttccgc gagacgaaga + 1201 cgaattctct agatatcgct caatactgac catttaaatc atacctgacc tccatagcag + 1261 aaagtcaaaa gcctccgacc ggaggctttt gacttgatcg gcacgtaaga ggttccaact + 1321 ttcaccataa tgaaataaga tcactaccgg gcgtattttt tgagttatcg agattttcag + 1381 gagctaagga agctaaaatg agccatattc aacgggaaac gtcttgctcg aggccgcgat + 1441 taaattccaa catggatgct gatttatatg ggtataaatg ggctcgcgat aatgtcgggc + 1501 aatcaggtgc gacaatctat cgattgtatg ggaagcccga tgcgccagag ttgtttctga + 1561 aacatggcaa aggtagcgtt gccaatgatg ttacagatga gatggtcagg ctaaactggc + 1621 tgacggaatt tatgcctctt ccgaccatca agcattttat ccgtactcct gatgatgcat + 1681 ggttactcac cactgcgatc ccagggaaaa cagcattcca ggtattagaa gaatatcctg + 1741 attcaggtga aaatattgtt gatgcgctgg cagtgttcct gcgccggttg cattcgattc + 1801 ctgtttgtaa ttgtcctttt aacggcgatc gcgtatttcg tctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p4_lac-o.gb b/tools/create_assembly_picklists/test-data/emma_parts/p4_lac-o.gb new file mode 100644 index 00000000..effeea5f --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p4_lac-o.gb @@ -0,0 +1,87 @@ +LOCUS . 1909 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + protein_bind 1160..1176 + /bound_moiety="lac repressor encoded by lacI" + /note="lac operator" + /note="The lac repressor binds to the lac operator to + inhibit transcription in E. coli. This inhibition can be + relieved by adding lactose or + isopropyl-beta-D-thiogalactopyranoside (IPTG)." + protein_bind 1229..1248 + /bound_moiety="lac repressor encoded by lacI" + /note="lac operator (symmetric)" + /note="The lac repressor binds to the lac operator to + inhibit transcription in E. coli. This inhibition can be + relieved by adding lactose or + isopropyl-beta-D-thiogalactopyranoside (IPTG). The + symmetric lac operator was optimized for tight binding of + lac repressor." + source 1154..1249 + /source="Exported" + misc_feature complement(1255..1260) + /note="BsmBI" + terminator 1327..1358 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1359..1461 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1254..1909 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgg gacagtcaat tgtgagcgga taacaattcc acagtcgacc ctaggttgtg + 1201 tcgcgagtgt tggatcccag ctgacaccaa ttgtgagcgc tcacaattct ccgcgagacg + 1261 aagacgaatt ctctagatat cgctcaatac tgaccattta aatcatacct gacctccata + 1321 gcagaaagtc aaaagcctcc gaccggaggc ttttgacttg atcggcacgt aagaggttcc + 1381 aactttcacc ataatgaaat aagatcacta ccgggcgtat tttttgagtt atcgagattt + 1441 tcaggagcta aggaagctaa aatgagccat attcaacggg aaacgtcttg ctcgaggccg + 1501 cgattaaatt ccaacatgga tgctgattta tatgggtata aatgggctcg cgataatgtc + 1561 gggcaatcag gtgcgacaat ctatcgattg tatgggaagc ccgatgcgcc agagttgttt + 1621 ctgaaacatg gcaaaggtag cgttgccaat gatgttacag atgagatggt caggctaaac + 1681 tggctgacgg aatttatgcc tcttccgacc atcaagcatt ttatccgtac tcctgatgat + 1741 gcatggttac tcaccactgc gatcccaggg aaaacagcat tccaggtatt agaagaatat + 1801 cctgattcag gtgaaaatat tgttgatgcg ctggcagtgt tcctgcgccg gttgcattcg + 1861 attcctgttt gtaattgtcc ttttaacggc gatcgcgtat ttcgtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p5_attb-bxb1.gb b/tools/create_assembly_picklists/test-data/emma_parts/p5_attb-bxb1.gb new file mode 100644 index 00000000..84a1e250 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p5_attb-bxb1.gb @@ -0,0 +1,76 @@ +LOCUS . 1855 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1156..1193 + /note="attB - BxB1" + misc_feature 1157..1170 + /note="B" + misc_feature complement(1179..1193) + /note="B'" + source 1154..1195 + /source="Exported" + misc_feature complement(1201..1206) + /note="BsmBI" + terminator 1273..1304 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1305..1407 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1200..1855 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgt ccgaaggctt gtcgacgacg gcggtctccg tcgtcaggat catcgccagc + 1201 gagacgaaga cgaattctct agatatcgct caatactgac catttaaatc atacctgacc + 1261 tccatagcag aaagtcaaaa gcctccgacc ggaggctttt gacttgatcg gcacgtaaga + 1321 ggttccaact ttcaccataa tgaaataaga tcactaccgg gcgtattttt tgagttatcg + 1381 agattttcag gagctaagga agctaaaatg agccatattc aacgggaaac gtcttgctcg + 1441 aggccgcgat taaattccaa catggatgct gatttatatg ggtataaatg ggctcgcgat + 1501 aatgtcgggc aatcaggtgc gacaatctat cgattgtatg ggaagcccga tgcgccagag + 1561 ttgtttctga aacatggcaa aggtagcgtt gccaatgatg ttacagatga gatggtcagg + 1621 ctaaactggc tgacggaatt tatgcctctt ccgaccatca agcattttat ccgtactcct + 1681 gatgatgcat ggttactcac cactgcgatc ccagggaaaa cagcattcca ggtattagaa + 1741 gaatatcctg attcaggtga aaatattgtt gatgcgctgg cagtgttcct gcgccggttg + 1801 cattcgattc ctgtttgtaa ttgtcctttt aacggcgatc gcgtatttcg tctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p5_attp-bxb1.gb b/tools/create_assembly_picklists/test-data/emma_parts/p5_attp-bxb1.gb new file mode 100644 index 00000000..16fcc84c --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p5_attp-bxb1.gb @@ -0,0 +1,77 @@ +LOCUS . 1869 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1156..1207 + /note="attP - BxB1" + misc_feature 1158..1176 + /note="P" + misc_feature complement(1186..1205) + /note="P'" + source 1154..1209 + /source="Exported" + misc_feature complement(1215..1220) + /note="BsmBI" + terminator 1287..1318 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1319..1421 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1214..1869 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgt ccgctgtggt ttgtctggtc aaccaccgcg gtctcagtgg tgtacggtac + 1201 aaacccatgc cagcgagacg aagacgaatt ctctagatat cgctcaatac tgaccattta + 1261 aatcatacct gacctccata gcagaaagtc aaaagcctcc gaccggaggc ttttgacttg + 1321 atcggcacgt aagaggttcc aactttcacc ataatgaaat aagatcacta ccgggcgtat + 1381 tttttgagtt atcgagattt tcaggagcta aggaagctaa aatgagccat attcaacggg + 1441 aaacgtcttg ctcgaggccg cgattaaatt ccaacatgga tgctgattta tatgggtata + 1501 aatgggctcg cgataatgtc gggcaatcag gtgcgacaat ctatcgattg tatgggaagc + 1561 ccgatgcgcc agagttgttt ctgaaacatg gcaaaggtag cgttgccaat gatgttacag + 1621 atgagatggt caggctaaac tggctgacgg aatttatgcc tcttccgacc atcaagcatt + 1681 ttatccgtac tcctgatgat gcatggttac tcaccactgc gatcccaggg aaaacagcat + 1741 tccaggtatt agaagaatat cctgattcag gtgaaaatat tgttgatgcg ctggcagtgt + 1801 tcctgcgccg gttgcattcg attcctgttt gtaattgtcc ttttaacggc gatcgcgtat + 1861 ttcgtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p5_k1-k1.gb b/tools/create_assembly_picklists/test-data/emma_parts/p5_k1-k1.gb new file mode 100644 index 00000000..7f64b670 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p5_k1-k1.gb @@ -0,0 +1,75 @@ +LOCUS . 1884 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1162..1183 + /note="K1" + misc_feature 1191..1212 + /note="K1" + source 1154..1224 + /source="Exported" + misc_feature complement(1230..1235) + /note="BsmBI" + terminator 1302..1333 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1334..1436 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1229..1884 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgt ccgcaaacaa agggtgtgaa cggtgatcac ccgagagcaa gggtgtgaac + 1201 ggtgatcacc cgcaaacaaa ttcgccagcg agacgaagac gaattctcta gatatcgctc + 1261 aatactgacc atttaaatca tacctgacct ccatagcaga aagtcaaaag cctccgaccg + 1321 gaggcttttg acttgatcgg cacgtaagag gttccaactt tcaccataat gaaataagat + 1381 cactaccggg cgtatttttt gagttatcga gattttcagg agctaaggaa gctaaaatga + 1441 gccatattca acgggaaacg tcttgctcga ggccgcgatt aaattccaac atggatgctg + 1501 atttatatgg gtataaatgg gctcgcgata atgtcgggca atcaggtgcg acaatctatc + 1561 gattgtatgg gaagcccgat gcgccagagt tgtttctgaa acatggcaaa ggtagcgttg + 1621 ccaatgatgt tacagatgag atggtcaggc taaactggct gacggaattt atgcctcttc + 1681 cgaccatcaa gcattttatc cgtactcctg atgatgcatg gttactcacc actgcgatcc + 1741 cagggaaaac agcattccag gtattagaag aatatcctga ttcaggtgaa aatattgttg + 1801 atgcgctggc agtgttcctg cgccggttgc attcgattcc tgtttgtaat tgtcctttta + 1861 acggcgatcg cgtatttcgt ctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p5_kt-weiss.gb b/tools/create_assembly_picklists/test-data/emma_parts/p5_kt-weiss.gb new file mode 100644 index 00000000..ed996fdc --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p5_kt-weiss.gb @@ -0,0 +1,75 @@ +LOCUS . 1896 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1162..1188 + /note="Kt" + misc_feature 1198..1224 + /note="Kt" + source 1154..1236 + /source="Exported" + misc_feature complement(1242..1247) + /note="BsmBI" + terminator 1314..1345 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1346..1448 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1241..1896 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgt ccgcaaacaa aggatccgtg atcggaaacg tgagatccaa agcaaaagga + 1201 tccgtgatcg gaaacgtgag atcccaaaca aattcgccag cgagacgaag acgaattctc + 1261 tagatatcgc tcaatactga ccatttaaat catacctgac ctccatagca gaaagtcaaa + 1321 agcctccgac cggaggcttt tgacttgatc ggcacgtaag aggttccaac tttcaccata + 1381 atgaaataag atcactaccg ggcgtatttt ttgagttatc gagattttca ggagctaagg + 1441 aagctaaaat gagccatatt caacgggaaa cgtcttgctc gaggccgcga ttaaattcca + 1501 acatggatgc tgatttatat gggtataaat gggctcgcga taatgtcggg caatcaggtg + 1561 cgacaatcta tcgattgtat gggaagcccg atgcgccaga gttgtttctg aaacatggca + 1621 aaggtagcgt tgccaatgat gttacagatg agatggtcag gctaaactgg ctgacggaat + 1681 ttatgcctct tccgaccatc aagcatttta tccgtactcc tgatgatgca tggttactca + 1741 ccactgcgat cccagggaaa acagcattcc aggtattaga agaatatcct gattcaggtg + 1801 aaaatattgt tgatgcgctg gcagtgttcc tgcgccggtt gcattcgatt cctgtttgta + 1861 attgtccttt taacggcgat cgcgtatttc gtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p6_atg_boxc.gb b/tools/create_assembly_picklists/test-data/emma_parts/p6_atg_boxc.gb new file mode 100644 index 00000000..1fac8383 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p6_atg_boxc.gb @@ -0,0 +1,79 @@ +LOCUS . 1886 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1186..1195 + /note="Kozak" + CDS 1192..1194 + /codon_start=1 + /note="ATG" + /translation="M" + misc_feature 1198..1221 + /note="BoxC/D" + source 1154..1226 + /source="Exported" + misc_feature complement(1232..1237) + /note="BsmBI" + terminator 1304..1335 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1336..1438 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1231..1886 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc cagaaccgtc agatccgcta gcgattacgt caattgccac catgggaggg + 1201 cgtgatgcga aagctgaccc tagcggcagc cgagacgaag acgaattctc tagatatcgc + 1261 tcaatactga ccatttaaat catacctgac ctccatagca gaaagtcaaa agcctccgac + 1321 cggaggcttt tgacttgatc ggcacgtaag aggttccaac tttcaccata atgaaataag + 1381 atcactaccg ggcgtatttt ttgagttatc gagattttca ggagctaagg aagctaaaat + 1441 gagccatatt caacgggaaa cgtcttgctc gaggccgcga ttaaattcca acatggatgc + 1501 tgatttatat gggtataaat gggctcgcga taatgtcggg caatcaggtg cgacaatcta + 1561 tcgattgtat gggaagcccg atgcgccaga gttgtttctg aaacatggca aaggtagcgt + 1621 tgccaatgat gttacagatg agatggtcag gctaaactgg ctgacggaat ttatgcctct + 1681 tccgaccatc aagcatttta tccgtactcc tgatgatgca tggttactca ccactgcgat + 1741 cccagggaaa acagcattcc aggtattaga agaatatcct gattcaggtg aaaatattgt + 1801 tgatgcgctg gcagtgttcc tgcgccggtt gcattcgatt cctgtttgta attgtccttt + 1861 taacggcgat cgcgtatttc gtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p6_kozak-atg.gb b/tools/create_assembly_picklists/test-data/emma_parts/p6_kozak-atg.gb new file mode 100644 index 00000000..222998d5 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p6_kozak-atg.gb @@ -0,0 +1,76 @@ +LOCUS . 1856 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1184..1195 + /note="Kozak" + CDS 1192..1194 + /codon_start=1 + /note="ATG" + /translation="M" + source 1154..1196 + /source="Exported" + misc_feature complement(1202..1207) + /note="BsmBI" + terminator 1274..1305 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1306..1408 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1201..1856 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc cagaaccgtc agatccgcta gagattacgc caaccgccac catgggcagc + 1201 cgagacgaag acgaattctc tagatatcgc tcaatactga ccatttaaat catacctgac + 1261 ctccatagca gaaagtcaaa agcctccgac cggaggcttt tgacttgatc ggcacgtaag + 1321 aggttccaac tttcaccata atgaaataag atcactaccg ggcgtatttt ttgagttatc + 1381 gagattttca ggagctaagg aagctaaaat gagccatatt caacgggaaa cgtcttgctc + 1441 gaggccgcga ttaaattcca acatggatgc tgatttatat gggtataaat gggctcgcga + 1501 taatgtcggg caatcaggtg cgacaatcta tcgattgtat gggaagcccg atgcgccaga + 1561 gttgtttctg aaacatggca aaggtagcgt tgccaatgat gttacagatg agatggtcag + 1621 gctaaactgg ctgacggaat ttatgcctct tccgaccatc aagcatttta tccgtactcc + 1681 tgatgatgca tggttactca ccactgcgat cccagggaaa acagcattcc aggtattaga + 1741 agaatatcct gattcaggtg aaaatattgt tgatgcgctg gcagtgttcc tgcgccggtt + 1801 gcattcgatt cctgtttgta attgtccttt taacggcgat cgcgtatttc gtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p6_nt-igkl sequence.gb b/tools/create_assembly_picklists/test-data/emma_parts/p6_nt-igkl sequence.gb new file mode 100644 index 00000000..bc088197 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p6_nt-igkl sequence.gb @@ -0,0 +1,83 @@ +LOCUS . 1886 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1154..1165 + /note="KozaK" + CDS 1162..1164 + /codon_start=1 + /note="ATG" + /translation="M" + CDS 1165..1224 + /codon_start=1 + /note="Ig-kappa leader" + /product="leader sequence from mouse immunoglobulin kappa + light chain" + /translation="ETDTLLLWVLLLWVPGSTGD" + source 1154..1226 + /source="Exported" + misc_feature complement(1232..1237) + /note="BsmBI" + terminator 1304..1335 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1336..1438 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1231..1886 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc cagccgccac catggaaaca gacacactgc tgctatgggt actgctgctc + 1201 tgggttccag gttccactgg tgacagcagc cgagacgaag acgaattctc tagatatcgc + 1261 tcaatactga ccatttaaat catacctgac ctccatagca gaaagtcaaa agcctccgac + 1321 cggaggcttt tgacttgatc ggcacgtaag aggttccaac tttcaccata atgaaataag + 1381 atcactaccg ggcgtatttt ttgagttatc gagattttca ggagctaagg aagctaaaat + 1441 gagccatatt caacgggaaa cgtcttgctc gaggccgcga ttaaattcca acatggatgc + 1501 tgatttatat gggtataaat gggctcgcga taatgtcggg caatcaggtg cgacaatcta + 1561 tcgattgtat gggaagcccg atgcgccaga gttgtttctg aaacatggca aaggtagcgt + 1621 tgccaatgat gttacagatg agatggtcag gctaaactgg ctgacggaat ttatgcctct + 1681 tccgaccatc aagcatttta tccgtactcc tgatgatgca tggttactca ccactgcgat + 1741 cccagggaaa acagcattcc aggtattaga agaatatcct gattcaggtg aaaatattgt + 1801 tgatgcgctg gcagtgttcc tgcgccggtt gcattcgatt cctgtttgta attgtccttt + 1861 taacggcgat cgcgtatttc gtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p6_nt-mls.gb b/tools/create_assembly_picklists/test-data/emma_parts/p6_nt-mls.gb new file mode 100644 index 00000000..66a2121a --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p6_nt-mls.gb @@ -0,0 +1,81 @@ +LOCUS . 1910 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1154..1161 + /note="KozaK" + CDS 1162..1164 + /codon_start=1 + /note="ATG" + /translation="M" + CDS 1165..1248 + /codon_start=1 + /note="MLS" + /translation="SVLTPLLLRGLTGSARRLPVPRAKIHSL" + source 1154..1250 + /source="Exported" + misc_feature complement(1256..1261) + /note="BsmBI" + terminator 1328..1359 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1360..1462 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1255..1910 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc cagccgccac catgagcgtg ctgacccccc tgctgctgcg cggcctgacc + 1201 ggcagcgccc gccgcctgcc cgtgccccgc gccaagatcc acagcctggg cagccgagac + 1261 gaagacgaat tctctagata tcgctcaata ctgaccattt aaatcatacc tgacctccat + 1321 agcagaaagt caaaagcctc cgaccggagg cttttgactt gatcggcacg taagaggttc + 1381 caactttcac cataatgaaa taagatcact accgggcgta ttttttgagt tatcgagatt + 1441 ttcaggagct aaggaagcta aaatgagcca tattcaacgg gaaacgtctt gctcgaggcc + 1501 gcgattaaat tccaacatgg atgctgattt atatgggtat aaatgggctc gcgataatgt + 1561 cgggcaatca ggtgcgacaa tctatcgatt gtatgggaag cccgatgcgc cagagttgtt + 1621 tctgaaacat ggcaaaggta gcgttgccaa tgatgttaca gatgagatgg tcaggctaaa + 1681 ctggctgacg gaatttatgc ctcttccgac catcaagcat tttatccgta ctcctgatga + 1741 tgcatggtta ctcaccactg cgatcccagg gaaaacagca ttccaggtat tagaagaata + 1801 tcctgattca ggtgaaaata ttgttgatgc gctggcagtg ttcctgcgcc ggttgcattc + 1861 gattcctgtt tgtaattgtc cttttaacgg cgatcgcgta tttcgtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p6_nt-myristoylation signal.gb b/tools/create_assembly_picklists/test-data/emma_parts/p6_nt-myristoylation signal.gb new file mode 100644 index 00000000..0565a832 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p6_nt-myristoylation signal.gb @@ -0,0 +1,81 @@ +LOCUS . 1865 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1154..1161 + /note="KozaK" + CDS 1162..1164 + /codon_start=1 + /note="ATG" + /translation="M" + CDS 1165..1203 + /codon_start=1 + /note="myristoylation signal" + /translation="GSSKSKPKDPSQR" + source 1154..1205 + /source="Exported" + misc_feature complement(1211..1216) + /note="BsmBI" + terminator 1283..1314 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1315..1417 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1210..1865 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc cagccgccac catggggagt agcaagagca agcctaagga ccccagccag + 1201 cgcggcagcc gagacgaaga cgaattctct agatatcgct caatactgac catttaaatc + 1261 atacctgacc tccatagcag aaagtcaaaa gcctccgacc ggaggctttt gacttgatcg + 1321 gcacgtaaga ggttccaact ttcaccataa tgaaataaga tcactaccgg gcgtattttt + 1381 tgagttatcg agattttcag gagctaagga agctaaaatg agccatattc aacgggaaac + 1441 gtcttgctcg aggccgcgat taaattccaa catggatgct gatttatatg ggtataaatg + 1501 ggctcgcgat aatgtcgggc aatcaggtgc gacaatctat cgattgtatg ggaagcccga + 1561 tgcgccagag ttgtttctga aacatggcaa aggtagcgtt gccaatgatg ttacagatga + 1621 gatggtcagg ctaaactggc tgacggaatt tatgcctctt ccgaccatca agcattttat + 1681 ccgtactcct gatgatgcat ggttactcac cactgcgatc ccagggaaaa cagcattcca + 1741 ggtattagaa gaatatcctg attcaggtga aaatattgtt gatgcgctgg cagtgttcct + 1801 gcgccggttg cattcgattc ctgtttgtaa ttgtcctttt aacggcgatc gcgtatttcg + 1861 tctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p6_nt-palm sequence.gb b/tools/create_assembly_picklists/test-data/emma_parts/p6_nt-palm sequence.gb new file mode 100644 index 00000000..94c9b493 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p6_nt-palm sequence.gb @@ -0,0 +1,81 @@ +LOCUS . 1883 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1154..1161 + /note="Kozak" + CDS 1162..1164 + /codon_start=1 + /note="ATG" + /translation="M" + CDS 1165..1221 + /codon_start=1 + /note="Palmitoylation sequence" + /translation="LCCMRRTKQVEKNDDDQKI" + source 1154..1223 + /source="Exported" + misc_feature complement(1229..1234) + /note="BsmBI" + terminator 1301..1332 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1333..1435 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1228..1883 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc cagccgccac catgctgtgc tgcatgcgcc gcaccaagca ggtggagaag + 1201 aacgacgacg accagaagat cggcagccga gacgaagacg aattctctag atatcgctca + 1261 atactgacca tttaaatcat acctgacctc catagcagaa agtcaaaagc ctccgaccgg + 1321 aggcttttga cttgatcggc acgtaagagg ttccaacttt caccataatg aaataagatc + 1381 actaccgggc gtattttttg agttatcgag attttcagga gctaaggaag ctaaaatgag + 1441 ccatattcaa cgggaaacgt cttgctcgag gccgcgatta aattccaaca tggatgctga + 1501 tttatatggg tataaatggg ctcgcgataa tgtcgggcaa tcaggtgcga caatctatcg + 1561 attgtatggg aagcccgatg cgccagagtt gtttctgaaa catggcaaag gtagcgttgc + 1621 caatgatgtt acagatgaga tggtcaggct aaactggctg acggaattta tgcctcttcc + 1681 gaccatcaag cattttatcc gtactcctga tgatgcatgg ttactcacca ctgcgatccc + 1741 agggaaaaca gcattccagg tattagaaga atatcctgat tcaggtgaaa atattgttga + 1801 tgcgctggca gtgttcctgc gccggttgca ttcgattcct gtttgtaatt gtccttttaa + 1861 cggcgatcgc gtatttcgtc tcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p6_nt-sv40_nls.gb b/tools/create_assembly_picklists/test-data/emma_parts/p6_nt-sv40_nls.gb new file mode 100644 index 00000000..b91fcabd --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p6_nt-sv40_nls.gb @@ -0,0 +1,82 @@ +LOCUS . 1847 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1154..1161 + /note="Kozak" + CDS 1162..1164 + /codon_start=1 + /note="ATG" + /translation="M" + CDS 1165..1185 + /codon_start=1 + /note="SV40 NLS" + /product="nuclear localization signal of SV40 large T + antigen" + /translation="PKKKRKV" + source 1154..1187 + /source="Exported" + misc_feature complement(1193..1198) + /note="BsmBI" + terminator 1265..1296 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1297..1399 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1192..1847 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc cagccgccac catgcctaag aagaaacgga aagtgggcag ccgagacgaa + 1201 gacgaattct ctagatatcg ctcaatactg accatttaaa tcatacctga cctccatagc + 1261 agaaagtcaa aagcctccga ccggaggctt ttgacttgat cggcacgtaa gaggttccaa + 1321 ctttcaccat aatgaaataa gatcactacc gggcgtattt tttgagttat cgagattttc + 1381 aggagctaag gaagctaaaa tgagccatat tcaacgggaa acgtcttgct cgaggccgcg + 1441 attaaattcc aacatggatg ctgatttata tgggtataaa tgggctcgcg ataatgtcgg + 1501 gcaatcaggt gcgacaatct atcgattgta tgggaagccc gatgcgccag agttgtttct + 1561 gaaacatggc aaaggtagcg ttgccaatga tgttacagat gagatggtca ggctaaactg + 1621 gctgacggaa tttatgcctc ttccgaccat caagcatttt atccgtactc ctgatgatgc + 1681 atggttactc accactgcga tcccagggaa aacagcattc caggtattag aagaatatcc + 1741 tgattcaggt gaaaatattg ttgatgcgct ggcagtgttc ctgcgccggt tgcattcgat + 1801 tcctgtttgt aattgtcctt ttaacggcga tcgcgtattt cgtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p7_bxb1.gb b/tools/create_assembly_picklists/test-data/emma_parts/p7_bxb1.gb new file mode 100644 index 00000000..9c3742bb --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p7_bxb1.gb @@ -0,0 +1,107 @@ +LOCUS . 3312 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + CDS 5..1501 + /codon_start=1 + /note="BxB1 intergase - human codon optimised" + /translation="RALVVIRLSRVTDATTSPERQLESCQQLCAQRGWDVVGVAEDLDV + SGAVDPFDRKRRPNLARWLAFEEQPFDVIVAYRVDRLTRSIRHLQQLVHWAEDHKKLVV + SATEAHFDTTTPFAAVVIALMGTVAQMELEAIKERNRSAAHFNIRAGKYRGSLPPWGYL + PTRVDGEWRLVPDPVQRERILEVYHRVVDNHEPLHLVAHDLNRRGVLSPKDYFAQLQGR + EPQGREWSATALKRSMISEAMLGYATLNGKTVRDDDGAPLVRAEPILTREQLEALRAEL + VKTSRAKPAVSTPSLLLRVLFCAVCGEPAYKFAGGGRKHPRYRCRSMGFPKHCGNGTVA + MAEWDAFCEEQVLDLLGDAERLEKVWVAGSDSAVELAEVNAELVDLTSLIGSPAYRAGS + PQREALDARIAALAARQEELEGLEARPSGWEWRETGQRFGDWWREQDTAAKNTWLRSMN + VRLTFDVRGGLTRTIDFGDLQEYEQHLRLGSVVERLHTGMS" + source 5..1503 + /source="Exported" + misc_feature complement(1509..1514) + /note="BsmBI" + terminator 1581..1612 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1613..1715 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1508..2163 + /source="Exported" + terminator 2555..2582 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(2594..3181) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 3203..3232 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 3306..3311 + /note="BsmBI" + source 2168..3312 + /source="Exported" +ORIGIN + 1 cagcagagca ctggtggtca tccgactgag tagggtcaca gacgcaacaa caagccccga + 61 acggcagctc gaaagctgtc agcagctgtg tgcccagcga ggatgggacg tggtcggagt + 121 ggcagaggat ctggacgtga gcggcgctgt cgatccattc gacagaaagc ggaggcccaa + 181 cctggcaagg tggctggctt tcgaggaaca gccctttgat gtgatcgtcg cctacagagt + 241 ggacaggctg acacgctcta ttcgacatct gcagcagctg gtgcattggg ccgaggacca + 301 caagaaactg gtggtcagtg caactgaagc ccacttcgat accacaactc cttttgccgc + 361 tgtggtcatc gcactgatgg gcaccgtggc ccagatggag ctggaagcta tcaaggagcg + 421 aaaccggagt gcagcccatt tcaatattcg ggccgggaaa tacagaggat cactgccccc + 481 ttggggctat ctgcctaccc gggtggatgg ggagtggaga ctggtgccag accccgtcca + 541 gagagagagg attctggaag tgtaccacag ggtggtcgat aaccacgaac cactgcatct + 601 ggtcgcccac gacctgaata ggcgcggcgt gctgagccca aaagattatt ttgctcagct + 661 gcagggaagg gagccacagg gacgagaatg gtccgctacc gccctgaagc ggagcatgat + 721 cagtgaggct atgctgggct acgcaactct gaatgggaaa accgtccggg acgatgacgg + 781 agcaccactg gtgagggctg agcctattct gacacgcgag cagctggaag ctctgcgggc + 841 agaactggtg aaaacctcca gagccaaacc tgccgtgagc accccaagcc tgctgctgag + 901 ggtgctgttc tgcgccgtct gtggggagcc agcatacaag tttgccggcg ggggaagaaa + 961 acatccccgc tatcgatgcc ggtctatggg attccctaag cactgtggaa acggcactgt + 1021 ggctatggcc gagtgggacg ccttttgtga ggaacaggtg ctggatctgc tgggcgacgc + 1081 cgagaggctg gaaaaagtgt gggtcgctgg cagcgactcc gctgtggagc tggcagaagt + 1141 caatgccgag ctggtggatc tgacctccct gatcggatct cctgcatata gggcaggctc + 1201 accacagcga gaagctctgg acgcacgaat tgctgcactg gcagctcgac aggaggaact + 1261 ggaggggctg gaagcacgac ctagcggatg ggagtggcga gaaacaggcc agcggtttgg + 1321 ggattggtgg agagagcagg acacagcagc caagaacact tggctgagaa gtatgaatgt + 1381 caggctgact ttcgatgtgc gcggcgggct gacccgaaca atcgattttg gcgacctgca + 1441 ggagtatgaa cagcacctga gactggggag cgtggtcgaa agactgcaca ctgggatgtc + 1501 atcaggccga gacgaagacg aattctctag atatcgctca atactgacca tttaaatcat + 1561 acctgacctc catagcagaa agtcaaaagc ctccgaccgg aggcttttga cttgatcggc + 1621 acgtaagagg ttccaacttt caccataatg aaataagatc actaccgggc gtattttttg + 1681 agttatcgag attttcagga gctaaggaag ctaaaatgag ccatattcaa cgggaaacgt + 1741 cttgctcgag gccgcgatta aattccaaca tggatgctga tttatatggg tataaatggg + 1801 ctcgcgataa tgtcgggcaa tcaggtgcga caatctatcg attgtatggg aagcccgatg + 1861 cgccagagtt gtttctgaaa catggcaaag gtagcgttgc caatgatgtt acagatgaga + 1921 tggtcaggct aaactggctg acggaattta tgcctcttcc gaccatcaag cattttatcc + 1981 gtactcctga tgatgcatgg ttactcacca ctgcgatccc agggaaaaca gcattccagg + 2041 tattagaaga atatcctgat tcaggtgaaa atattgttga tgcgctggca gtgttcctgc + 2101 gccggttgca ttcgattcct gtttgtaatt gtccttttaa cggcgatcgc gtatttcgtc + 2161 tcgctcaggc gcaatcacga atgaataacg gtttggttgg tgcgagtgat tttgatgacg + 2221 agcgtaatgg ctggcctgtt gaacaagtct ggaaagaaat gcataagctt ttgccattct + 2281 caccggattc agtcgtcact catggtgatt tctcacttga taaccttatt tttgacgagg + 2341 ggaaattaat aggttgtatt gatgttggac gagtcggaat cgcagaccga taccaggatc + 2401 ttgccatcct atggaactgc ctcggtgagt tttctccttc attacagaaa cggctttttc + 2461 aaaaatatgg tattgataat cctgatatga ataaattgca gtttcacttg atgctcgatg + 2521 agtttttcta atgagggccc aaatgtaatc acctggctca ccttcgggtg ggcctttctg + 2581 cgttgctggc gtttttccat aggctccgcc cccctgacga gcatcacaaa aatcgatgct + 2641 caagtcagag gtggcgaaac ccgacaggac tataaagata ccaggcgttt ccccctggaa + 2701 gctccctcgt gcgctctcct gttccgaccc tgccgcttac cggatacctg tccgcctttc + 2761 tcccttcggg aagcgtggcg ctttctcata gctcacgctg taggtatctc agttcggtgt + 2821 aggtcgttcg ctccaagctg ggctgtgtgc acgaaccccc cgttcagccc gaccgctgcg + 2881 ccttatccgg taactatcgt cttgagtcca acccggtaag acacgactta tcgccactgg + 2941 cagcagccac tggtaacagg attagcagag cgaggtatgt aggcggtgct acagagttct + 3001 tgaagtggtg gcctaactac ggctacacta gaagaacagt atttggtatc tgcgctctgc + 3061 tgaagccagt tacctcggaa aaagagttgg tagctcttga tccggcaaac aaaccaccgc + 3121 tggtagcggt ggtttttttg tttgcaagca gcagattacg cgcagaaaaa aaggatctca + 3181 agaagatcct ttgattttct accgaagaaa ggcccacccg tgaaggtgag ccagtgagtt + 3241 gattgcagtc cagttacgct ggagtctgag gctcgtcctg aatgatatca agcttgaatt + 3301 cgttacgtct cg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p7_l7ae-weiss.gb b/tools/create_assembly_picklists/test-data/emma_parts/p7_l7ae-weiss.gb new file mode 100644 index 00000000..7073006f --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p7_l7ae-weiss.gb @@ -0,0 +1,82 @@ +LOCUS . 2169 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + CDS 1154..1507 + /codon_start=1 + /note="L7Ae (Weiss)" + /translation="YVRFEVPEDMQNEALSLLEKVRESGKVKKGTNETTKAVERGLAKL + VYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKSKNDLGRAVGIEVPCASAAIINEGELRK + ELGSLVEKIKGLQK" + source 1154..1509 + /source="Exported" + misc_feature complement(1515..1520) + /note="BsmBI" + terminator 1587..1618 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1619..1721 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1514..2169 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc agctacgtga gatttgaggt tcctgaggac atgcagaacg aagctctgag + 1201 tctgctggag aaggttaggg agagcggtaa ggtaaagaaa ggtaccaacg aaacgacaaa + 1261 ggctgtggag aggggactgg caaagctcgt ttacatcgca gaggatgttg acccgcctga + 1321 gatcgttgct catctgcccc tcctctgcga ggagaagaat gtgccgtaca tttacgttaa + 1381 aagcaagaac gaccttggaa gggctgtggg cattgaggtg ccatgcgctt cggcagcgat + 1441 aatcaacgag ggagagctga gaaaggagct tggaagcctt gtggagaaga ttaaaggcct + 1501 tcagaagtca ggccgagacg aagacgaatt ctctagatat cgctcaatac tgaccattta + 1561 aatcatacct gacctccata gcagaaagtc aaaagcctcc gaccggaggc ttttgacttg + 1621 atcggcacgt aagaggttcc aactttcacc ataatgaaat aagatcacta ccgggcgtat + 1681 tttttgagtt atcgagattt tcaggagcta aggaagctaa aatgagccat attcaacggg + 1741 aaacgtcttg ctcgaggccg cgattaaatt ccaacatgga tgctgattta tatgggtata + 1801 aatgggctcg cgataatgtc gggcaatcag gtgcgacaat ctatcgattg tatgggaagc + 1861 ccgatgcgcc agagttgttt ctgaaacatg gcaaaggtag cgttgccaat gatgttacag + 1921 atgagatggt caggctaaac tggctgacgg aatttatgcc tcttccgacc atcaagcatt + 1981 ttatccgtac tcctgatgat gcatggttac tcaccactgc gatcccaggg aaaacagcat + 2041 tccaggtatt agaagaatat cctgattcag gtgaaaatat tgttgatgcg ctggcagtgt + 2101 tcctgcgccg gttgcattcg attcctgttt gtaattgtcc ttttaacggc gatcgcgtat + 2161 ttcgtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p7_l7ae.gb b/tools/create_assembly_picklists/test-data/emma_parts/p7_l7ae.gb new file mode 100644 index 00000000..c34989f1 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p7_l7ae.gb @@ -0,0 +1,87 @@ +LOCUS . 2409 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + CDS 1154..1747 + /codon_start=1 + /note="L7Ae" + /translation="SPILGYWKIKGLVQPTRLLLEYLEEKYEEHLYERDEGDKWRNKKF + ELGLEFPNLPYYIDGDVKLTQSMAIIRYIADKHNMYVRFEVPEDMQNEALSLLEKVRES + GKVKKGTNETTKAVERGLAKLVYIAEDVDPPEIVAHLPLLCEEKNVPYIYVKSKNDLGR + AVGIEVPCASAAIINEGELRKELGSLVEKIKGLQK" + source 1154..1749 + /source="Exported" + misc_feature complement(1755..1760) + /note="BsmBI" + terminator 1827..1858 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1859..1961 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1754..2409 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc agcagcccca tcctgggcta ctggaagatc aagggcctgg tgcagcccac + 1201 ccgcctgctg ctggagtacc tggaggagaa gtacgaggag cacctgtacg agcgcgacga + 1261 gggcgacaag tggcgcaaca agaagttcga gctgggcctg gagttcccca acctgcccta + 1321 ctacatcgac ggcgacgtga agctgaccca gagcatggcc atcatccgct acatcgccga + 1381 caagcacaac atgtacgtgc gcttcgaggt gcccgaggac atgcagaacg aggccctgag + 1441 cctgctggag aaggtgcgcg agagcggcaa ggtgaagaag ggcaccaacg aaaccaccaa + 1501 ggccgtggag cgcggcctgg ccaagctggt gtacatcgcc gaggacgtgg acccccccga + 1561 gatcgtggcc cacctgcccc tgctgtgcga ggagaagaac gtgccctaca tctacgtgaa + 1621 gagcaagaac gacctgggcc gcgccgtggg catcgaggtg ccctgcgcca gcgccgccat + 1681 catcaacgag ggcgagctgc gcaaggagct gggcagcctg gtggagaaga tcaagggcct + 1741 gcagaagtca ggccgagacg aagacgaatt ctctagatat cgctcaatac tgaccattta + 1801 aatcatacct gacctccata gcagaaagtc aaaagcctcc gaccggaggc ttttgacttg + 1861 atcggcacgt aagaggttcc aactttcacc ataatgaaat aagatcacta ccgggcgtat + 1921 tttttgagtt atcgagattt tcaggagcta aggaagctaa aatgagccat attcaacggg + 1981 aaacgtcttg ctcgaggccg cgattaaatt ccaacatgga tgctgattta tatgggtata + 2041 aatgggctcg cgataatgtc gggcaatcag gtgcgacaat ctatcgattg tatgggaagc + 2101 ccgatgcgcc agagttgttt ctgaaacatg gcaaaggtag cgttgccaat gatgttacag + 2161 atgagatggt caggctaaac tggctgacgg aatttatgcc tcttccgacc atcaagcatt + 2221 ttatccgtac tcctgatgat gcatggttac tcaccactgc gatcccaggg aaaacagcat + 2281 tccaggtatt agaagaatat cctgattcag gtgaaaatat tgttgatgcg ctggcagtgt + 2341 tcctgcgccg gttgcattcg attcctgttt gtaattgtcc ttttaacggc gatcgcgtat + 2401 ttcgtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p7_laci.gb b/tools/create_assembly_picklists/test-data/emma_parts/p7_laci.gb new file mode 100644 index 00000000..dcf007b8 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p7_laci.gb @@ -0,0 +1,98 @@ +LOCUS . 2892 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + CDS 1154..2230 + /codon_start=1 + /note="LacI- human codon optimized" + /translation="KPVTLYDVAEYAGVSYQTVSRVVNQASHVSAKTREKVEAAMAELN + YIPNRVAQQLAGKQSLLIGVATSSLALHAPSQIVAAIKSRADQLGASVVVSMVERSGVE + ACKAAVHNLLAQRVSGLIINYPLDDQDAIAVEAACTNVPALFLDVSDQTPINSIIFSHE + DGTRLGVEHLVALGHQQIALLAGPLSSVSARLRLAGWHKYLTRNQIQPIAEREGDWSAM + SGFQQTMQMLNEGIVPTAMLVANDQMALGAMRAITESGLRVGADISVVGYDDTEDSSCY + IPPLTTIKQDFRLLGQTSVDRLLQLSQGQAVKGNQLLPVSLVKRKTTLAPNTQTASPRA + LADSLMQLARQVSRLESGQ" + source 1154..2232 + /source="Exported" + misc_feature complement(2238..2243) + /note="BsmBI" + terminator 2310..2341 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 2342..2444 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 2237..2892 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc agcaagcccg tgaccctgta cgacgtggcc gagtacgccg gcgtgagcta + 1201 ccagaccgtg agccgcgtgg tgaaccaggc cagccacgtg agcgccaaga cccgcgagaa + 1261 ggtggaggcc gccatggccg agctgaatta catcccaaat cgcgtggccc agcagctggc + 1321 cggcaagcag agcctgctga tcggagtggc aacaagcagc ctggccctgc acgcacctag + 1381 ccagatcgtg gcagccatca agagccgcgc cgaccagctg ggagccagcg tggttgtgag + 1441 catggtggag cgcagcggag tggaggcctg caaggccgcc gtgcacaacc tgctggcaca + 1501 gcgcgtgagc ggactgatca tcaactaccc tctggacgac caggacgcca tcgcagtgga + 1561 agcagcctgc acaaacgtgc ccgcactgtt tctggatgtg agcgatcaga cccccatcaa + 1621 cagcatcatc ttcagccacg aagatggcac ccgcctggga gtggagcacc tggtggccct + 1681 gggccaccag cagatcgcac tgctggccgg cccactgagc agcgtgagcg cacgcctgcg + 1741 cctggcaggc tggcacaagt acctgacccg caaccagatc cagcctatcg ccgaacgcga + 1801 aggcgattgg agcgccatga gcggatttca gcagaccatg cagatgctga acgagggaat + 1861 cgtgcctacc gccatgctgg tggccaacga ccagatggcc ctgggagcca tgcgcgccat + 1921 caccgagagc ggcctgcgcg tgggagcaga catcagcgtg gtgggatacg acgacaccga + 1981 agacagcagc tgctacatcc ctcctctgac aaccatcaag caggacttcc gcctgctggg + 2041 ccagaccagc gtggaccgcc tgctgcagct gagccaggga caggccgtga agggaaacca + 2101 gctgctgcct gtgagcctgg tgaagcgcaa gaccaccctg gcacccaaca cccagaccgc + 2161 cagcccccgc gccctggccg acagcctgat gcagctggcc cgccaggtga gccgcctgga + 2221 aagcggacag tcaggccgag acgaagacga attctctaga tatcgctcaa tactgaccat + 2281 ttaaatcata cctgacctcc atagcagaaa gtcaaaagcc tccgaccgga ggcttttgac + 2341 ttgatcggca cgtaagaggt tccaactttc accataatga aataagatca ctaccgggcg + 2401 tattttttga gttatcgaga ttttcaggag ctaaggaagc taaaatgagc catattcaac + 2461 gggaaacgtc ttgctcgagg ccgcgattaa attccaacat ggatgctgat ttatatgggt + 2521 ataaatgggc tcgcgataat gtcgggcaat caggtgcgac aatctatcga ttgtatggga + 2581 agcccgatgc gccagagttg tttctgaaac atggcaaagg tagcgttgcc aatgatgtta + 2641 cagatgagat ggtcaggcta aactggctga cggaatttat gcctcttccg accatcaagc + 2701 attttatccg tactcctgat gatgcatggt tactcaccac tgcgatccca gggaaaacag + 2761 cattccaggt attagaagaa tatcctgatt caggtgaaaa tattgttgat gcgctggcag + 2821 tgttcctgcg ccggttgcat tcgattcctg tttgtaattg tccttttaac ggcgatcgcg + 2881 tatttcgtct cg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p7_mcherry.gb b/tools/create_assembly_picklists/test-data/emma_parts/p7_mcherry.gb new file mode 100644 index 00000000..9ae26506 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p7_mcherry.gb @@ -0,0 +1,89 @@ +LOCUS . 2520 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + CDS 1154..1858 + /codon_start=1 + /note="mCherry- codon optimized" + /translation="VSKGEEDNMAIIKEFMRFKVHMEGSVNGHEFEIEGEGEGRPYEGT + QTAKLKVTKGGPLPFAWDILSPQFMYGSKAYVKHPADIPDYLKLSFPEGFKWERVMNFE + DGGVVTVTQDSSLQDGEFIYKVKLRGTNFPSDGPVMQKKTMGWEASSERMYPEDGALKG + EIKQRLKLKDGGHYDAEVKTTYKAKKPVQLPGAYNVNIKLDITSHNEDYTIVEQYERAE + GRHSTGGMDELYK" + source 1154..1860 + /source="Exported" + misc_feature complement(1866..1871) + /note="BsmBI" + terminator 1938..1969 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1970..2072 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1865..2520 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc agcgtgagca agggcgagga ggacaacatg gccatcatca aggagttcat + 1201 gcgcttcaag gtgcacatgg agggcagcgt gaacggccac gagttcgaga tcgagggcga + 1261 gggcgagggc cgcccctacg agggcaccca gaccgccaag ctgaaggtga ccaagggcgg + 1321 ccccctgccc ttcgcctggg acatcctgag cccccagttc atgtacggca gcaaggccta + 1381 cgtgaagcac cccgccgaca tccccgacta cctgaagctg agcttccccg agggcttcaa + 1441 gtgggagcgc gtgatgaact tcgaggacgg cggcgtggtg accgtgaccc aggacagcag + 1501 cctgcaggac ggcgagttca tctacaaggt gaagctgcgc ggcaccaact tccccagcga + 1561 cggccccgtg atgcagaaga agaccatggg ctgggaggcc agcagcgagc gcatgtaccc + 1621 cgaggacggc gccctgaagg gcgagatcaa gcagcgcctg aagctgaagg acggcggcca + 1681 ctacgacgcc gaggtgaaga ccacctacaa ggccaagaag cccgtgcagc tgcccggcgc + 1741 ctacaacgtg aacatcaagc tggacatcac cagccacaac gaggactaca ccatcgtgga + 1801 gcagtacgag cgcgccgagg gccgccacag caccggcggc atggacgagc tgtacaagtc + 1861 aggccgagac gaagacgaat tctctagata tcgctcaata ctgaccattt aaatcatacc + 1921 tgacctccat agcagaaagt caaaagcctc cgaccggagg cttttgactt gatcggcacg + 1981 taagaggttc caactttcac cataatgaaa taagatcact accgggcgta ttttttgagt + 2041 tatcgagatt ttcaggagct aaggaagcta aaatgagcca tattcaacgg gaaacgtctt + 2101 gctcgaggcc gcgattaaat tccaacatgg atgctgattt atatgggtat aaatgggctc + 2161 gcgataatgt cgggcaatca ggtgcgacaa tctatcgatt gtatgggaag cccgatgcgc + 2221 cagagttgtt tctgaaacat ggcaaaggta gcgttgccaa tgatgttaca gatgagatgg + 2281 tcaggctaaa ctggctgacg gaatttatgc ctcttccgac catcaagcat tttatccgta + 2341 ctcctgatga tgcatggtta ctcaccactg cgatcccagg gaaaacagca ttccaggtat + 2401 tagaagaata tcctgattca ggtgaaaata ttgttgatgc gctggcagtg ttcctgcgcc + 2461 ggttgcattc gattcctgtt tgtaattgtc cttttaacgg cgatcgcgta tttcgtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p7_mkate2.gb b/tools/create_assembly_picklists/test-data/emma_parts/p7_mkate2.gb new file mode 100644 index 00000000..a2afc979 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p7_mkate2.gb @@ -0,0 +1,90 @@ +LOCUS . 2508 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + CDS 1154..1846 + /codon_start=1 + /gene="mKate2" + /note="mKate2" + /translation="VSELIKENMHMKLYMEGTVNNHHFKCTSEGEGKPYEGTQTMRIKA + VEGGPLPFAFDILATSFMYGSKTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGVLTA + TQDTSLQDGCLIYNVKIRGVNFPSNGPVMQKKTLGWEASTETLYPADGGLEGRADMALK + LVGGGHLICNLKTTYRSKKPAKNLKMPGVYYVDRRLERIKEADKETYVEQHEVAVARYC + DLPSKLGHR" + source 1154..1848 + /source="Exported" + misc_feature complement(1854..1859) + /note="BsmBI" + terminator 1926..1957 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1958..2060 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1853..2508 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc agcgtgagcg agctgattaa ggagaacatg cacatgaagc tgtacatgga + 1201 gggcaccgtg aacaaccacc acttcaagtg cacatccgag ggcgaaggca agccctacga + 1261 gggcacccag accatgagaa tcaaggcggt cgagggcggc cctctcccct tcgccttcga + 1321 catcctggct accagcttca tgtacggcag caaaaccttc atcaaccaca cccagggcat + 1381 ccccgacttc tttaagcagt ccttccccga gggcttcaca tgggagagag tcaccacata + 1441 cgaagacggg ggcgtgctga ccgctaccca ggacaccagc ctccaggacg gctgcctcat + 1501 ctacaacgtc aagatcagag gggtgaactt cccatccaac ggccctgtga tgcagaagaa + 1561 aacactcggc tgggaggcct ccaccgaaac cctgtacccc gctgacggcg gcctggaagg + 1621 cagagccgac atggccctga agctcgtggg cgggggccac ctgatctgca acttgaagac + 1681 cacatacaga tccaagaaac ccgctaagaa cctcaagatg cccggcgtct actatgtgga + 1741 cagaagactg gaaagaatca aggaggccga caaagaaacc tacgtcgagc agcacgaggt + 1801 ggctgtggcc agatactgcg acctccctag caaactgggg cacagatcag gccgagacga + 1861 agacgaattc tctagatatc gctcaatact gaccatttaa atcatacctg acctccatag + 1921 cagaaagtca aaagcctccg accggaggct tttgacttga tcggcacgta agaggttcca + 1981 actttcacca taatgaaata agatcactac cgggcgtatt ttttgagtta tcgagatttt + 2041 caggagctaa ggaagctaaa atgagccata ttcaacggga aacgtcttgc tcgaggccgc + 2101 gattaaattc caacatggat gctgatttat atgggtataa atgggctcgc gataatgtcg + 2161 ggcaatcagg tgcgacaatc tatcgattgt atgggaagcc cgatgcgcca gagttgtttc + 2221 tgaaacatgg caaaggtagc gttgccaatg atgttacaga tgagatggtc aggctaaact + 2281 ggctgacgga atttatgcct cttccgacca tcaagcattt tatccgtact cctgatgatg + 2341 catggttact caccactgcg atcccaggga aaacagcatt ccaggtatta gaagaatatc + 2401 ctgattcagg tgaaaatatt gttgatgcgc tggcagtgtt cctgcgccgg ttgcattcga + 2461 ttcctgtttg taattgtcct tttaacggcg atcgcgtatt tcgtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p7_mneogreen.gb b/tools/create_assembly_picklists/test-data/emma_parts/p7_mneogreen.gb new file mode 100644 index 00000000..472698f4 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p7_mneogreen.gb @@ -0,0 +1,91 @@ +LOCUS . 2520 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + CDS 1154..1858 + /codon_start=1 + /note="mNeonGreen" + /product="bright monomeric yellow-green fluorescent protein + derived from LanYFP (Shaner et al., 2013)" + /translation="VSKGEEDNMASLPATHELHIFGSINGVDFDMVGQGTGNPNDGYEE + LNLKSTKGDLQFSPWILVPHIGYGFHQYLPYPDGMSPFQAAMVDGSGYQVHRTMQFEDG + ASLTVNYRYTYEGSHIKGEAQVKGTGFPADGPVMTNSLTAADWCRSKKTYPNDKTIIST + FKWSYTTGNGKRYRSTARTTYTFAKPMAANYLKNQPMYVFRKTELKHSKTELNFKEWQK + AFTDVMGMDELYK" + source 1154..1860 + /source="Exported" + misc_feature complement(1866..1871) + /note="BsmBI" + terminator 1938..1969 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1970..2072 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1865..2520 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc agcgtgagca agggcgagga ggataacatg gcctctctcc cagcgacaca + 1201 tgagttacac atctttggct ccatcaacgg tgtggacttt gacatggtgg gtcagggcac + 1261 cggcaatcca aatgatggtt atgaggagtt aaacctgaag tccaccaagg gtgacctcca + 1321 gttctccccc tggattctgg tccctcatat cgggtatggc ttccatcagt acctgcccta + 1381 ccctgacggg atgtcgcctt tccaggccgc catggtagat ggctccggat accaagtcca + 1441 tcgcacaatg cagtttgaag atggtgcctc ccttactgtt aactaccgct acacctacga + 1501 gggaagccac atcaaaggag aggcccaggt gaaggggact ggtttccctg ctgacggtcc + 1561 tgtgatgacc aactcgctga ccgctgcgga ctggtgcagg tcgaagaaga cttaccccaa + 1621 cgacaaaacc atcatcagta cctttaagtg gagttacacc actggaaatg gcaagcgcta + 1681 ccggagcact gcgcggacca cctacacctt tgccaagcca atggcggcta actatctgaa + 1741 gaaccagccg atgtacgtgt tccgtaagac ggagctcaag cactccaaga ccgagctcaa + 1801 cttcaaggag tggcaaaagg cctttaccga tgtgatgggc atggacgagc tgtacaagtc + 1861 aggccgagac gaagacgaat tctctagata tcgctcaata ctgaccattt aaatcatacc + 1921 tgacctccat agcagaaagt caaaagcctc cgaccggagg cttttgactt gatcggcacg + 1981 taagaggttc caactttcac cataatgaaa taagatcact accgggcgta ttttttgagt + 2041 tatcgagatt ttcaggagct aaggaagcta aaatgagcca tattcaacgg gaaacgtctt + 2101 gctcgaggcc gcgattaaat tccaacatgg atgctgattt atatgggtat aaatgggctc + 2161 gcgataatgt cgggcaatca ggtgcgacaa tctatcgatt gtatgggaag cccgatgcgc + 2221 cagagttgtt tctgaaacat ggcaaaggta gcgttgccaa tgatgttaca gatgagatgg + 2281 tcaggctaaa ctggctgacg gaatttatgc ctcttccgac catcaagcat tttatccgta + 2341 ctcctgatga tgcatggtta ctcaccactg cgatcccagg gaaaacagca ttccaggtat + 2401 tagaagaata tcctgattca ggtgaaaata ttgttgatgc gctggcagtg ttcctgcgcc + 2461 ggttgcattc gattcctgtt tgtaattgtc cttttaacgg cgatcgcgta tttcgtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p7_mruby2.gb b/tools/create_assembly_picklists/test-data/emma_parts/p7_mruby2.gb new file mode 100644 index 00000000..4fe1106c --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p7_mruby2.gb @@ -0,0 +1,93 @@ +LOCUS . 2523 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + CDS 1154..1861 + /codon_start=1 + /note="mRuby2" + /product="monomeric red fluorescent protein derived from + mRuby, with improved photophysical properties (Lam et al., + 2012)" + /translation="VSKGEELIKENMRMKVVMEGSVNGHQFKCTGEGEGNPYMGTQTMR + IKVIEGGPLPFAFDILATSFMYGSRTFIKYPKGIPDFFKQSFPEGFTWERVTRYEDGGV + VTVMQDTSLEDGCLVYHVQVRGVNFPSNGPVMQKKTKGWEPNTEMMYPADGGLRGYTHM + ALKVDGGGHLSCSFVTTYRSKKTVGNIKMPGIHAVDHRLERLEESDNEMFVVQREHAVA + KFAGLGGGMDELYK" + source 1154..1863 + /source="Exported" + misc_feature complement(1869..1874) + /note="BsmBI" + terminator 1941..1972 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1973..2075 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1868..2523 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc agcgtgtcta agggcgaaga gctgatcaag gaaaatatgc gtatgaaggt + 1201 ggtcatggaa ggttcggtca acggccacca attcaaatgc acaggtgaag gagaaggcaa + 1261 tccgtacatg ggaactcaaa ccatgaggat caaagtcatc gagggaggac ccctgccatt + 1321 tgcctttgac attcttgcca cgtcgttcat gtatggcagc cgtactttta tcaagtaccc + 1381 gaaaggcatt cctgatttct ttaaacagtc ctttcctgag ggttttactt gggaaagagt + 1441 tacgagatac gaagatggtg gagtcgtcac cgtcatgcag gacaccagcc ttgaggatgg + 1501 ctgtctcgtt taccacgtcc aagtcagagg ggtaaacttt ccctccaatg gtcccgtgat + 1561 gcagaagaag accaagggtt gggagcctaa tacagagatg atgtatccag cagatggtgg + 1621 tctgagggga tacactcata tggcactgaa agttgatggt ggtggccatc tgtcttgctc + 1681 tttcgtaaca acttacaggt caaaaaagac cgtcgggaac atcaagatgc ccggtatcca + 1741 tgccgttgat caccgcctgg aaaggttaga ggaaagtgac aatgaaatgt tcgtagtaca + 1801 acgcgaacac gcagttgcca agttcgccgg gcttggtggt gggatggacg agctgtacaa + 1861 gtcaggccga gacgaagacg aattctctag atatcgctca atactgacca tttaaatcat + 1921 acctgacctc catagcagaa agtcaaaagc ctccgaccgg aggcttttga cttgatcggc + 1981 acgtaagagg ttccaacttt caccataatg aaataagatc actaccgggc gtattttttg + 2041 agttatcgag attttcagga gctaaggaag ctaaaatgag ccatattcaa cgggaaacgt + 2101 cttgctcgag gccgcgatta aattccaaca tggatgctga tttatatggg tataaatggg + 2161 ctcgcgataa tgtcgggcaa tcaggtgcga caatctatcg attgtatggg aagcccgatg + 2221 cgccagagtt gtttctgaaa catggcaaag gtagcgttgc caatgatgtt acagatgaga + 2281 tggtcaggct aaactggctg acggaattta tgcctcttcc gaccatcaag cattttatcc + 2341 gtactcctga tgatgcatgg ttactcacca ctgcgatccc agggaaaaca gcattccagg + 2401 tattagaaga atatcctgat tcaggtgaaa atattgttga tgcgctggca gtgttcctgc + 2461 gccggttgca ttcgattcct gtttgtaatt gtccttttaa cggcgatcgc gtatttcgtc + 2521 tcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p7_mtagbfp2.gb b/tools/create_assembly_picklists/test-data/emma_parts/p7_mtagbfp2.gb new file mode 100644 index 00000000..ce3ec918 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p7_mtagbfp2.gb @@ -0,0 +1,93 @@ +LOCUS . 2523 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + CDS 1154..1861 + /codon_start=1 + /note="mTagBFP2" + /note="mammalian codon-optimized" + /product="enhanced monomeric blue fluorescent protein + (Subach et al., 2011)" + /translation="VSKGEELIKENMHMKLYMEGTVDNHHFKCTSEGEGKPYEGTQTMR + IKVVEGGPLPFAFDILATSFLYGSKTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGV + LTATQDTSLQDGCLIYNVKIRGVNFTSNGPVMQKKTLGWEAFTETLYPADGGLEGRNDM + ALKLVGGSHLIANAKTTYRSKKPAKNLKMPGVYYVDYRLERIKEANNETYVEQHEVAVA + RYCDLPSKLGHKLN" + source 1154..1863 + /source="Exported" + misc_feature complement(1869..1874) + /note="BsmBI" + terminator 1941..1972 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1973..2075 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1868..2523 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcgc agcgtgtcta agggcgaaga gctgattaag gagaacatgc acatgaagct + 1201 gtacatggag ggcaccgtgg acaaccatca cttcaagtgc acatccgagg gcgaaggcaa + 1261 gccctacgag ggcacccaga ccatgagaat caaggtggtc gagggcggcc ctctcccctt + 1321 cgccttcgac atcctggcta ctagcttcct ctacggcagc aagaccttca tcaaccacac + 1381 ccagggcatc cccgacttct tcaagcagtc cttccctgag ggcttcacat gggagagagt + 1441 caccacatac gaagacgggg gcgtgctgac cgctacccag gacaccagcc tccaggacgg + 1501 ctgcctcatc tacaacgtca agatcagagg ggtgaacttc acatccaacg gccctgtgat + 1561 gcagaagaaa acactcggct gggaggcctt caccgaaacg ctgtaccccg ctgacggcgg + 1621 cctggaaggc agaaacgaca tggccctgaa gctcgtgggc gggagccatc tgatcgcaaa + 1681 cgccaagacc acatatagat ccaagaaacc cgctaagaac ctcaagatgc ctggcgtcta + 1741 ctatgtggac tacagactgg aaagaatcaa ggaggccaac aacgaaacct acgtcgagca + 1801 gcacgaggtg gcagtggcca gatactgcga cctccctagc aaactggggc acaagcttaa + 1861 ttcaggccga gacgaagacg aattctctag atatcgctca atactgacca tttaaatcat + 1921 acctgacctc catagcagaa agtcaaaagc ctccgaccgg aggcttttga cttgatcggc + 1981 acgtaagagg ttccaacttt caccataatg aaataagatc actaccgggc gtattttttg + 2041 agttatcgag attttcagga gctaaggaag ctaaaatgag ccatattcaa cgggaaacgt + 2101 cttgctcgag gccgcgatta aattccaaca tggatgctga tttatatggg tataaatggg + 2161 ctcgcgataa tgtcgggcaa tcaggtgcga caatctatcg attgtatggg aagcccgatg + 2221 cgccagagtt gtttctgaaa catggcaaag gtagcgttgc caatgatgtt acagatgaga + 2281 tggtcaggct aaactggctg acggaattta tgcctcttcc gaccatcaag cattttatcc + 2341 gtactcctga tgatgcatgg ttactcacca ctgcgatccc agggaaaaca gcattccagg + 2401 tattagaaga atatcctgat tcaggtgaaa atattgttga tgcgctggca gtgttcctgc + 2461 gccggttgca ttcgattcct gtttgtaatt gtccttttaa cggcgatcgc gtatttcgtc + 2521 tcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p8_linker1.gb b/tools/create_assembly_picklists/test-data/emma_parts/p8_linker1.gb new file mode 100644 index 00000000..899a0b3d --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p8_linker1.gb @@ -0,0 +1,75 @@ +LOCUS . 1864 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + CDS 1814..1864 + /codon_start=1 + /note="Linker 1" + /translation="SGLRSGSGGGSASGGSG" + source 1814..1864 + /source="Exported" +ORIGIN + 1 gcgtcgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcga ggctctggac tcagatctgg cagcggagga ggcagcgcat ctggcggaag + 1861 cgga +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p8_linker2.gb b/tools/create_assembly_picklists/test-data/emma_parts/p8_linker2.gb new file mode 100644 index 00000000..14901f38 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p8_linker2.gb @@ -0,0 +1,74 @@ +LOCUS . 1849 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + CDS 1814..1849 + /codon_start=1 + /note="Linker 2" + /translation="GSAGSAAGSGEF" + source 1814..1849 + /source="Exported" +ORIGIN + 1 gcgtcgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcga ggcggcagcg ccggcagcgc cgccggcagc ggcgagttc +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p8_p2a.gb b/tools/create_assembly_picklists/test-data/emma_parts/p8_p2a.gb new file mode 100644 index 00000000..7d26387f --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p8_p2a.gb @@ -0,0 +1,80 @@ +LOCUS . 1870 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + CDS 1814..1870 + /codon_start=1 + /note="P2A-Porcine teschovirus-1" + /note="Eukaryotic ribosomes fail to insert a peptide bond + between the Gly and Pro residues, yielding separate + polypeptides." + /product="2A peptide from porcine teschovirus-1 + polyprotein" + /translation="ATNFSLLKQAGDVEENPGP" + source 1814..1870 + /source="Exported" +ORIGIN + 1 gcgtcgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcga ggcgctacta acttcagcct gctgaagcag gctggcgacg tggaggagaa + 1861 ccctggacct +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p8a_ct-kdel.gb b/tools/create_assembly_picklists/test-data/emma_parts/p8a_ct-kdel.gb new file mode 100644 index 00000000..ca190ad8 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p8a_ct-kdel.gb @@ -0,0 +1,75 @@ +LOCUS . 1863 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + CDS 1814..1828 + /codon_start=1 + /note="KDEL" + /translation="KDEL" + source 1814..1863 + /source="Exported" +ORIGIN + 1 atcccgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcga ggcaaggacg agctgtaagc ggccgcgact ctagatcata atcagccata + 1861 cca +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p8b_ires2.gb b/tools/create_assembly_picklists/test-data/emma_parts/p8b_ires2.gb new file mode 100644 index 00000000..565bd9ba --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p8b_ires2.gb @@ -0,0 +1,84 @@ +LOCUS . 2427 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + terminator 392..419 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + rep_origin complement(431..1018) + /direction=LEFT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 1040..1069 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + misc_feature 1143..1148 + /note="BsmBI" + source 5..1149 + /source="Exported" + misc_feature 1182..1767 + /note="IRES2" + /note="internal ribosome entry site (IRES) of the + encephalomyocarditis virus (EMCV)" + source 1154..1767 + /source="Exported" + misc_feature complement(1773..1778) + /note="BsmBI" + terminator 1845..1876 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + promoter 1877..1979 + /note="cat promoter" + /note="promoter of the E. coli cat gene" + source 1772..2427 + /source="Exported" +ORIGIN + 1 ctcaggcgca atcacgaatg aataacggtt tggttggtgc gagtgatttt gatgacgagc + 61 gtaatggctg gcctgttgaa caagtctgga aagaaatgca taagcttttg ccattctcac + 121 cggattcagt cgtcactcat ggtgatttct cacttgataa ccttattttt gacgagggga + 181 aattaatagg ttgtattgat gttggacgag tcggaatcgc agaccgatac caggatcttg + 241 ccatcctatg gaactgcctc ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa + 301 aatatggtat tgataatcct gatatgaata aattgcagtt tcacttgatg ctcgatgagt + 361 ttttctaatg agggcccaaa tgtaatcacc tggctcacct tcgggtgggc ctttctgcgt + 421 tgctggcgtt tttccatagg ctccgccccc ctgacgagca tcacaaaaat cgatgctcaa + 481 gtcagaggtg gcgaaacccg acaggactat aaagatacca ggcgtttccc cctggaagct + 541 ccctcgtgcg ctctcctgtt ccgaccctgc cgcttaccgg atacctgtcc gcctttctcc + 601 cttcgggaag cgtggcgctt tctcatagct cacgctgtag gtatctcagt tcggtgtagg + 661 tcgttcgctc caagctgggc tgtgtgcacg aaccccccgt tcagcccgac cgctgcgcct + 721 tatccggtaa ctatcgtctt gagtccaacc cggtaagaca cgacttatcg ccactggcag + 781 cagccactgg taacaggatt agcagagcga ggtatgtagg cggtgctaca gagttcttga + 841 agtggtggcc taactacggc tacactagaa gaacagtatt tggtatctgc gctctgctga + 901 agccagttac ctcggaaaaa gagttggtag ctcttgatcc ggcaaacaaa ccaccgctgg + 961 tagcggtggt ttttttgttt gcaagcagca gattacgcgc agaaaaaaag gatctcaaga + 1021 agatcctttg attttctacc gaagaaaggc ccacccgtga aggtgagcca gtgagttgat + 1081 tgcagtccag ttacgctgga gtctgaggct cgtcctgaat gatatcaagc ttgaattcgt + 1141 tacgtctcga tcccgctcga taagcttgat atcgaattcc gcccctctcc ctcccccccc + 1201 cctaacgtta ctggccgaag ccgcttggaa taaggccggt gtgcgtttgt ctatatgtta + 1261 ttttccacca tattgccgtc ttttggcaat gtgagggccc ggaaacctgg ccctgtcttc + 1321 ttgacgagca ttcctagggg tctttcccct ctcgccaaag gaatgcaagg tctgttgaat + 1381 gtcgtgaagg aagcagttcc tctggaagct tcttgaagac aaacaacgtc tgtagcgacc + 1441 ctttgcaggc agcggaaccc cccacctggc gacaggtgcc tctgcggcca aaagccacgt + 1501 gtataagata cacctgcaaa ggcggcacaa ccccagtgcc acgttgtgag ttggatagtt + 1561 gtggaaagag tcaaatggct ctcctcaagc gtattcaaca aggggctgaa ggatgcccag + 1621 aaggtacccc attgtatggg atctgatctg gggcctcggt gcacatgctt tacatgtgtt + 1681 tagtcgaggt taaaaaacgt ctaggccccc cgaaccacgg ggacgtggtt ttcctttgaa + 1741 aaacacgatg ataatatggc cacaaccgcg tcgagacgaa gacgaattct ctagatatcg + 1801 ctcaatactg accatttaaa tcatacctga cctccatagc agaaagtcaa aagcctccga + 1861 ccggaggctt ttgacttgat cggcacgtaa gaggttccaa ctttcaccat aatgaaataa + 1921 gatcactacc gggcgtattt tttgagttat cgagattttc aggagctaag gaagctaaaa + 1981 tgagccatat tcaacgggaa acgtcttgct cgaggccgcg attaaattcc aacatggatg + 2041 ctgatttata tgggtataaa tgggctcgcg ataatgtcgg gcaatcaggt gcgacaatct + 2101 atcgattgta tgggaagccc gatgcgccag agttgtttct gaaacatggc aaaggtagcg + 2161 ttgccaatga tgttacagat gagatggtca ggctaaactg gctgacggaa tttatgcctc + 2221 ttccgaccat caagcatttt atccgtactc ctgatgatgc atggttactc accactgcga + 2281 tcccagggaa aacagcattc caggtattag aagaatatcc tgattcaggt gaaaatattg + 2341 ttgatgcgct ggcagtgttc ctgcgccggt tgcattcgat tcctgtttgt aattgtcctt + 2401 ttaacggcga tcgcgtattt cgtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p9_a-tubulin.gb b/tools/create_assembly_picklists/test-data/emma_parts/p9_a-tubulin.gb new file mode 100644 index 00000000..fd009df2 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p9_a-tubulin.gb @@ -0,0 +1,103 @@ +LOCUS . 3175 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + CDS 7..1359 + /codon_start=1 + /note="a-Tubulin" + /translation="VRECISIHVGQAGVQIGNACWELYCLEHGIQPDGQMPSDKTIGGG + DDSFNTFFSETGAGKHVPRAVFVDLEPTVIDEVRTGTYRQLFHPEQLITGKEDAANNYA + RGHYTIGKEIIDLVLDRIRKLADQCTGLQGFLVFHSFGGGTGSGFTSLLMERLSVDYGK + KSKLEFSIYPAPQVSTAVVEPYNSILTTHTTLEHSDCAFMVDNEAIYDICRRNLDIERP + TYTNLNRLISQIVSSITASLRFDGALNVDLTEFQTNLVPYPRIHFPLATYAPVISAEKA + YHEQLSVAEITNACFEPANQMVKCDPRHGKYMACCLLYRGDVVPKDVNAAIATIKTKRS + IQFVDWCPTGFKVGINYQPPTVVPGGDLAKVQRAVCMLSNTTAIAEAWARLDHKFDLMY + AKRAFVHWYVGEGMEEGEFSEAREDMAALEKDYEEVGVDSVEGEGEEEGEEY" + source 5..1366 + /source="Exported" + misc_feature complement(1372..1377) + /note="BsmBI" + terminator 1452..1481 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 1503..2090 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 2102..2129 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 1371..2516 + /source="Exported" + promoter complement(2969..3071) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 3072..3103 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 3169..3174 + /note="BsmBI" + source 2521..3175 + /source="Exported" +ORIGIN + 1 gcgtccgtgc gtgagtgcat ctccatccac gttggccagg ctggtgtcca gattggcaat + 61 gcctgctggg agctctactg cctggaacac ggcatccagc ccgatggcca gatgccaagt + 121 gacaagacca ttgggggagg agatgactcc ttcaacacct tcttcagtga aacgggcgct + 181 ggcaagcacg tgccccgggc tgtgtttgta gacttggaac ccacagtcat tgatgaagtt + 241 cgcactggca cctaccgcca gctcttccac cctgagcagc tcatcacagg caaggaagat + 301 gctgccaata actatgcccg agggcactac accattggca aggagatcat tgaccttgtg + 361 ttggaccgaa ttcgcaagct ggctgaccag tgcaccggtc ttcagggctt cttggttttc + 421 cacagctttg gtgggggaac tggttctggg ttcacctccc tgctcatgga acgcctctca + 481 gttgattatg gcaagaagtc caagctggag ttctccattt acccagcacc ccaggtttcc + 541 acagctgtag ttgagcccta caactccatc ctcaccaccc acaccaccct ggagcactct + 601 gattgtgcct tcatggtaga caatgaggcc atctatgaca tctgtcgtag aaacctcgat + 661 atcgagcgcc caacctacac taaccttaac cgccttatta gccagattgt gtcctccatc + 721 actgcttccc tgagatttga tggagccctg aatgttgacc tgacagaatt ccagaccaac + 781 ctggtgccct acccccgcat ccacttccct ctggccacat atgcccctgt catctctgct + 841 gagaaagcct accatgaaca gctttctgta gcagagatca ccaatgcttg ctttgagcca + 901 gccaaccaga tggtgaaatg tgaccctcgc catggtaaat acatggcttg ctgcctgttg + 961 taccgtggtg acgtggttcc caaagatgtc aatgctgcca ttgccaccat caaaaccaag + 1021 cgcagcatcc agtttgtgga ttggtgcccc actggcttca aggttggcat caactaccag + 1081 cctcccactg tggtgcctgg tggcgacctg gccaaggtac agagagctgt gtgcatgctg + 1141 agcaacacca cagccattgc tgaggcctgg gctcgcctgg accacaagtt tgacctgatg + 1201 tatgccaagc gtgcctttgt tcactggtac gtgggtgagg ggatggagga aggcgagttt + 1261 tcagaggccc gtgaagatat ggctgccctt gagaaggatt atgaggaggt tggtgtggat + 1321 tctgttgaag gagagggtga ggaagaagga gaggaatact aataactgct cgagacgaaa + 1381 acgaattcaa gcttgatatc attcaggacg agcctcagac tccagcgtaa ctggactgca + 1441 atcaactcac tggctcacct tcacgggtgg gcctttcttc ggtagaaaat caaaggatct + 1501 tcttgagatc ctttttttct gcgcgtaatc tgctgcttgc aaacaaaaaa accaccgcta + 1561 ccagcggtgg tttgtttgcc ggatcaagag ctaccaactc tttttccgag gtaactggct + 1621 tcagcagagc gcagatacca aatactgttc ttctagtgta gccgtagtta ggccaccact + 1681 tcaagaactc tgtagcaccg cctacatacc tcgctctgct aatcctgtta ccagtggctg + 1741 ctgccagtgg cgataagtcg tgtcttaccg ggttggactc aagacgatag ttaccggata + 1801 aggcgcagcg gtcgggctga acggggggtt cgtgcacaca gcccagcttg gagcgaacga + 1861 cctacaccga actgagatac ctacagcgtg agctatgaga aagcgccacg cttcccgaag + 1921 ggagaaaggc ggacaggtat ccggtaagcg gcagggtcgg aacaggagag cgcacgaggg + 1981 agcttccagg gggaaacgcc tggtatcttt atagtcctgt cgggtttcgc cacctctgac + 2041 ttgagcatcg atttttgtga tgctcgtcag gggggcggag cctatggaaa aacgccagca + 2101 acgcagaaag gcccacccga aggtgagcca ggtgattaca tttgggccct cattagaaaa + 2161 actcatcgag catcaagtga aactgcaatt tattcatatc aggattatca ataccatatt + 2221 tttgaaaaag ccgtttctgt aatgaaggag aaaactcacc gaggcagttc cataggatgg + 2281 caagatcctg gtatcggtct gcgattccga ctcgtccaac atcaatacaa cctattaatt + 2341 tcccctcgtc aaaaataagg ttatcaagtg agaaatcacc atgagtgacg actgaatccg + 2401 gtgagaatgg caaaagctta tgcatttctt tccagacttg ttcaacaggc cagccattac + 2461 gctcgtcatc aaaatcactc gcaccaacca aaccgttatt cattcgtgat tgcgcctgag + 2521 cgagacgaaa tacgcgatcg ccgttaaaag gacaattaca aacaggaatc gaatgcaacc + 2581 ggcgcaggaa cactgccagc gcatcaacaa tattttcacc tgaatcagga tattcttcta + 2641 atacctggaa tgctgttttc cctgggatcg cagtggtgag taaccatgca tcatcaggag + 2701 tacggataaa atgcttgatg gtcggaagag gcataaattc cgtcagccag tttagcctga + 2761 ccatctcatc tgtaacatca ttggcaacgc tacctttgcc atgtttcaga aacaactctg + 2821 gcgcatcggg cttcccatac aatcgataga ttgtcgcacc tgattgcccg acattatcgc + 2881 gagcccattt atacccatat aaatcagcat ccatgttgga atttaatcgc ggcctcgagc + 2941 aagacgtttc ccgttgaata tggctcattt tagcttcctt agctcctgaa aatctcgata + 3001 actcaaaaaa tacgcccggt agtgatctta tttcattatg gtgaaagttg gaacctctta + 3061 cgtgccgatc aagtcaaaag cctccggtcg gaggcttttg actttctgct atggaggtca + 3121 ggtatgattt aaatggtcag tattgagcga tatctagaga attcgtcacg tctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p9_bsdr.gb b/tools/create_assembly_picklists/test-data/emma_parts/p9_bsdr.gb new file mode 100644 index 00000000..7ca87539 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p9_bsdr.gb @@ -0,0 +1,82 @@ +LOCUS . 2214 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + CDS 1816..2208 + /codon_start=1 + /note="BSDR- Human codon opt" + /translation="AKPLSQEESTLIERATATINSIPISEDYSVASAALSSDGRIFTGV + NVYHFTGGPCAELVVLGTAAAAAAGNLTCIVAIGNENRGILSPCGRCRQVLLDLHPGIK + AIVKDSDGQPTAVGIRELLPSGYVWEG" + source 1814..2214 + /source="Exported" +ORIGIN + 1 tgctcgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcgg cgtccgccaa gcctctgagc caggaggaga gcaccctgat cgagcgcgcc + 1861 accgccacca tcaacagcat ccctatcagc gaagactaca gcgtggccag cgccgctctg + 1921 agcagcgacg gccgcatctt cacaggagtg aacgtgtacc acttcaccgg aggaccttgc + 1981 gccgaactgg tggtgctggg caccgctgcc gctgctgccg ctggaaacct gacctgcatc + 2041 gtggccatcg gcaacgagaa ccgcggaatc ctgagccctt gcggccgctg ccgccaggtg + 2101 ctgctggacc tgcaccccgg catcaaggcc atcgtgaagg acagcgacgg ccagcccacc + 2161 gccgtgggca tccgcgagct gctgcccagc ggctacgtgt gggaaggcta ataa +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p9_dmrc.gb b/tools/create_assembly_picklists/test-data/emma_parts/p9_dmrc.gb new file mode 100644 index 00000000..bdb40c93 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p9_dmrc.gb @@ -0,0 +1,83 @@ +LOCUS . 2101 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + CDS 1816..2094 + /codon_start=1 + /note="FRB* (DmrC)" + /note="binds synthetic ligands such as AP21967" + /product="T2098L mutant of FKBP-rapamycin binding domain of + human FRAP" + /translation="ILWHEMWHEGLEEASRLYFGERNVKGMFEVLEPLHAMMERGPQTL + KETSFNQAYGRDLMEAQEWCRKYMKSGNVKDLLQAWDLYYHVFRRISK" + source 1814..2101 + /source="Exported" +ORIGIN + 1 tgctcgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcgg cgtccatcct ctggcatgag atgtggcatg aaggcctgga agaggcatct + 1861 cgtttgtact ttggggaaag gaacgtgaaa ggcatgtttg aggtgctgga gcccttgcat + 1921 gctatgatgg aacggggccc ccagactctg aaggaaacat cctttaatca ggcctatggt + 1981 cgagatttaa tggaggccca agagtggtgc aggaagtaca tgaaatcagg gaatgtcaag + 2041 gacctcctcc aagcctggga cctctattat catgtgttcc gacgaatctc aaagtaataa + 2101 c +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p9_firefly luciferase.gb b/tools/create_assembly_picklists/test-data/emma_parts/p9_firefly luciferase.gb new file mode 100644 index 00000000..94e63fc0 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p9_firefly luciferase.gb @@ -0,0 +1,120 @@ +LOCUS . 3549 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + CDS 7..1653 + /codon_start=1 + /note="Firefly luciferase" + /translation="EDAKNIKKGPAPRYPLEDGTAGEQLHKAMKRYAQVPGTIAFTDAH + IEVNITYAEYFEMSVRLAEAMKRYGLNTNHRIVVCSENSLQFFMPVLGALFIGVAVAPA + NDIYNERELLNSMNISQPTVVFVSKKGLQKILNVQKKLPIIQKIIIMDSKTDYQGFQSM + YTFVTSHLPPGFNEYDFKPESFDRDKTIALIMNSSGSTGLPKGVALPHRTACVRFSHAR + DPIFGNQIKPDTAILSVVPFHHGFGMFTTLGYLICGFRVVLMYRFEEELFLRSLQDYKI + QTALLVPTLFSFFAKSTLIDKYDLSNLHEIASGGAPLSKEVGEAVAKRFHLPGIRQGYG + LTETTSAILITPEGDDKPGAVGKVVPFFEAKVVDLDTGKTLGVNQRGELCVRGPMIMSG + YVNNPEATNALIDKDGWLHSGDIAYWDEDEHFFIVDRLKSLIKYKGYQVAPAELESILL + QHPNIRDAGVAGLPDDDAGELPAAVVVLEHGKTMTEKEIVDYVASQVTTAKKLRGGVVF + VDEVPKGLTGKLDARKIREILIKAKKGGKIAV" + CDS 1654..1668 + /codon_start=1 + /note="Linker" + /translation="SGGGS" + CDS 1669..1734 + /codon_start=1 + /note="3XFLAG" + /translation="DYKDHDGDYKDHDIDYKDDDDK" + source 5..1740 + /source="Exported" + misc_feature complement(1746..1751) + /note="BsmBI" + terminator 1826..1855 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 1877..2464 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 2476..2503 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 1745..2890 + /source="Exported" + promoter complement(3343..3445) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 3446..3477 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 3543..3548 + /note="BsmBI" + source 2895..3549 + /source="Exported" +ORIGIN + 1 gcgtccgagg acgccaagaa catcaagaag ggaccagccc ccagataccc cctggaggac + 61 ggcacagccg gcgagcagct gcacaaggcc atgaagcggt acgcccaggt gccaggcacc + 121 atcgccttca ccgacgccca catcgaggtg aacatcacct acgccgagta cttcgagatg + 181 agcgtgcggc tggccgaggc catgaagcgg tacggcctga acaccaacca ccgcatcgtg + 241 gtttgcagcg aaaacagcct gcagttcttt atgccagttc tgggagcact gttcatcgga + 301 gttgcagtgg ccccagcaaa cgacatctac aacgaacgcg agctgctgaa ctccatgaac + 361 atcagccagc caaccgttgt gttcgtgagc aagaaaggcc tgcagaagat tctgaatgtg + 421 cagaagaagc tgccaatcat tcagaagatc attatcatgg acagcaagac cgattaccag + 481 ggcttccaga gcatgtacac cttcgtgacc agccacctgc ccccaggctt caacgagtac + 541 gacttcaagc ccgagagctt cgaccgggac aagaccatcg ccctgatcat gaacagcagc + 601 ggcagcaccg gcctgcccaa gggcgtggcc ctgccccacc ggaccgcctg cgtgcggttc + 661 agccacgcca gggaccccat cttcggcaac cagatcaagc cagacaccgc tatcctgagc + 721 gttgtgccat tccaccacgg cttcggcatg ttcaccaccc tgggctacct gatctgcggc + 781 ttccgggtgg tgctgatgta caggttcgag gaggagctgt tcctgcggag cctgcaggac + 841 tacaagatcc agaccgccct gctggtgccc accctgttca gcttcttcgc caagagcacc + 901 ctgatcgaca agtacgacct gagcaacctg cacgagatcg cctctggcgg agccccactg + 961 agcaaggagg tgggcgaggc cgtggccaag cggttccacc tgccaggcat ccggcagggc + 1021 tacgggctga ccgaaaccac tagcgccatc ctgatcaccc ccgagggcga cgacaagccc + 1081 ggagccgtgg gcaaggtggt tccattcttt gaggccaaag ttgtggacct ggataccggg + 1141 aagaccctgg gcgtgaacca gagaggcgag ctgtgcgtga gaggccccat gatcatgagc + 1201 ggctacgtga acaaccccga ggccaccaac gccctgatcg acaaggatgg ctggctgcac + 1261 agcggcgaca tcgcctactg ggatgaggac gagcacttct ttatcgtgga tcggctgaag + 1321 agcctgatca aatacaaggg ctaccaggtg gccccagccg agctggagag catcctgctg + 1381 cagcacccca acatccggga cgccggagtg gccggactgc ccgacgacga cgccggagag + 1441 ctgccagccg ccgtggtggt gctggagcac ggcaagacca tgaccgagaa ggagatcgtg + 1501 gactacgtgg ccagccaggt gaccaccgcc aaaaagctga gaggaggcgt ggtcttcgtg + 1561 gatgaagtgc ccaagggcct gaccgggaag ctggacgcca gaaagatccg ggagatcctg + 1621 atcaaggcca agaagggcgg caagatcgca gtgagcggag gcgggagcga ctacaaagac + 1681 catgacggtg attataaaga tcatgacatc gattacaagg atgacgatga caagtaataa + 1741 tgctcgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 1801 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 1861 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 1921 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 1981 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 2041 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 2101 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 2161 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 2221 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 2281 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 2341 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 2401 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 2461 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 2521 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 2581 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 2641 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 2701 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 2761 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 2821 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 2881 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 2941 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 3001 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 3061 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 3121 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 3181 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 3241 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 3301 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 3361 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 3421 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 3481 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 3541 cacgtctcg +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p9_mneogreen.gb b/tools/create_assembly_picklists/test-data/emma_parts/p9_mneogreen.gb new file mode 100644 index 00000000..d50858d5 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p9_mneogreen.gb @@ -0,0 +1,92 @@ +LOCUS . 2526 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + CDS 1816..2520 + /codon_start=1 + /note="mNeonGreen" + /product="bright monomeric yellow-green fluorescent protein + derived from LanYFP (Shaner et al., 2013)" + /translation="VSKGEEDNMASLPATHELHIFGSINGVDFDMVGQGTGNPNDGYEE + LNLKSTKGDLQFSPWILVPHIGYGFHQYLPYPDGMSPFQAAMVDGSGYQVHRTMQFEDG + ASLTVNYRYTYEGSHIKGEAQVKGTGFPADGPVMTNSLTAADWCRSKKTYPNDKTIIST + FKWSYTTGNGKRYRSTARTTYTFAKPMAANYLKNQPMYVFRKTELKHSKTELNFKEWQK + AFTDVMGMDELYK" + source 1814..2526 + /source="Exported" +ORIGIN + 1 tgctcgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcgg cgtccgtgag caagggcgag gaggataaca tggcctctct cccagcgaca + 1861 catgagttac acatctttgg ctccatcaac ggtgtggact ttgacatggt gggtcagggc + 1921 accggcaatc caaatgatgg ttatgaggag ttaaacctga agtccaccaa gggtgacctc + 1981 cagttctccc cctggattct ggtccctcat atcgggtatg gcttccatca gtacctgccc + 2041 taccctgacg ggatgtcgcc tttccaggcc gccatggtag atggctccgg ataccaagtc + 2101 catcgcacaa tgcagtttga agatggtgcc tcccttactg ttaactaccg ctacacctac + 2161 gagggaagcc acatcaaagg agaggcccag gtgaagggga ctggtttccc tgctgacggt + 2221 cctgtgatga ccaactcgct gaccgctgcg gactggtgca ggtcgaagaa gacttacccc + 2281 aacgacaaaa ccatcatcag tacctttaag tggagttaca ccactggaaa tggcaagcgc + 2341 taccggagca ctgcgcggac cacctacacc tttgccaagc caatggcggc taactatctg + 2401 aagaaccagc cgatgtacgt gttccgtaag acggagctca agcactccaa gaccgagctc + 2461 aacttcaagg agtggcaaaa ggcctttacc gatgtgatgg gcatggacga gctgtacaag + 2521 taataa +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p9_mruby2.gb b/tools/create_assembly_picklists/test-data/emma_parts/p9_mruby2.gb new file mode 100644 index 00000000..0d0be80c --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p9_mruby2.gb @@ -0,0 +1,93 @@ +LOCUS . 2529 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + CDS 1816..2523 + /codon_start=1 + /note="mRuby2" + /product="monomeric red fluorescent protein derived from + mRuby, with improved photophysical properties (Lam et al., + 2012)" + /translation="VSKGEELIKENMRMKVVMEGSVNGHQFKCTGEGEGNPYMGTQTMR + IKVIEGGPLPFAFDILATSFMYGSRTFIKYPKGIPDFFKQSFPEGFTWERVTRYEDGGV + VTVMQDTSLEDGCLVYHVQVRGVNFPSNGPVMQKKTKGWEPNTEMMYPADGGLRGYTHM + ALKVDGGGHLSCSFVTTYRSKKTVGNIKMPGIHAVDHRLERLEESDNEMFVVQREHAVA + KFAGLGGGMDELYK" + source 1814..2529 + /source="Exported" +ORIGIN + 1 tgctcgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcgg cgtccgtgtc taagggcgaa gagctgatca aggaaaatat gcgtatgaag + 1861 gtggtcatgg aaggttcggt caacggccac caattcaaat gcacaggtga aggagaaggc + 1921 aatccgtaca tgggaactca aaccatgagg atcaaagtca tcgagggagg acccctgcca + 1981 tttgcctttg acattcttgc cacgtcgttc atgtatggca gccgtacttt tatcaagtac + 2041 ccgaaaggca ttcctgattt ctttaaacag tcctttcctg agggttttac ttgggaaaga + 2101 gttacgagat acgaagatgg tggagtcgtc accgtcatgc aggacaccag ccttgaggat + 2161 ggctgtctcg tttaccacgt ccaagtcaga ggggtaaact ttccctccaa tggtcccgtg + 2221 atgcagaaga agaccaaggg ttgggagcct aatacagaga tgatgtatcc agcagatggt + 2281 ggtctgaggg gatacactca tatggcactg aaagttgatg gtggtggcca tctgtcttgc + 2341 tctttcgtaa caacttacag gtcaaaaaag accgtcggga acatcaagat gcccggtatc + 2401 catgccgttg atcaccgcct ggaaaggtta gaggaaagtg acaatgaaat gttcgtagta + 2461 caacgcgaac acgcagttgc caagttcgcc gggcttggtg gtgggatgga cgagctgtac + 2521 aagtaataa +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p9_mtagbfp2.gb b/tools/create_assembly_picklists/test-data/emma_parts/p9_mtagbfp2.gb new file mode 100644 index 00000000..27e87130 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p9_mtagbfp2.gb @@ -0,0 +1,93 @@ +LOCUS . 2526 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + CDS 1816..2523 + /codon_start=1 + /note="mTagBFP2" + /note="mammalian codon-optimized" + /product="enhanced monomeric blue fluorescent protein + (Subach et al., 2011)" + /translation="VSKGEELIKENMHMKLYMEGTVDNHHFKCTSEGEGKPYEGTQTMR + IKVVEGGPLPFAFDILATSFLYGSKTFINHTQGIPDFFKQSFPEGFTWERVTTYEDGGV + LTATQDTSLQDGCLIYNVKIRGVNFTSNGPVMQKKTLGWEAFTETLYPADGGLEGRNDM + ALKLVGGSHLIANAKTTYRSKKPAKNLKMPGVYYVDYRLERIKEANNETYVEQHEVAVA + RYCDLPSKLGHKLN" + source 1814..2526 + /source="Exported" +ORIGIN + 1 tgctcgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcgg cgtccgtgtc taagggcgaa gagctgatta aggagaacat gcacatgaag + 1861 ctgtacatgg agggcaccgt ggacaaccat cacttcaagt gcacatccga gggcgaaggc + 1921 aagccctacg agggcaccca gaccatgaga atcaaggtgg tcgagggcgg ccctctcccc + 1981 ttcgccttcg acatcctggc tactagcttc ctctacggca gcaagacctt catcaaccac + 2041 acccagggca tccccgactt cttcaagcag tccttccctg agggcttcac atgggagaga + 2101 gtcaccacat acgaagacgg gggcgtgctg accgctaccc aggacaccag cctccaggac + 2161 ggctgcctca tctacaacgt caagatcaga ggggtgaact tcacatccaa cggccctgtg + 2221 atgcagaaga aaacactcgg ctgggaggcc ttcaccgaaa cgctgtaccc cgctgacggc + 2281 ggcctggaag gcagaaacga catggccctg aagctcgtgg gcgggagcca tctgatcgca + 2341 aacgccaaga ccacatatag atccaagaaa cccgctaaga acctcaagat gcctggcgtc + 2401 tactatgtgg actacagact ggaaagaatc aaggaggcca acaacgaaac ctacgtcgag + 2461 cagcacgagg tggcagtggc cagatactgc gacctcccta gcaaactggg gcacaagctt + 2521 aattaa +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p9_neor.gb b/tools/create_assembly_picklists/test-data/emma_parts/p9_neor.gb new file mode 100644 index 00000000..35eb993b --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p9_neor.gb @@ -0,0 +1,94 @@ +LOCUS . 2628 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + CDS 1816..2628 + /codon_start=1 + /note="KanR/NeoR" + /note="confers resistance to kanamycin in bacteria or G418 + (Geneticin(R)) in eukaryotes" + /product="aminoglycoside phosphotransferase" + /translation="SHIQRETSCSRPRLNSNMDADLYGYKWARDNVGQSGATIYRLYGK + PDAPELFLKHGKGSVANDVTDEMVRLNWLTEFMPLPTIKHFIRTPDDAWLLTTAIPGKT + AFQVLEEYPDSGENIVDALAVFLRRLHSIPVCNCPFNSDRVFRLAQAQSRMNNGLVDAS + DFDDERNGWPVEQVWKEMHKLLPFSPDSVVTHGDFSLDNLIFDEGKLIGCIDVGRVGIA + DRYQDLAILWNCLGEFSPSLQKRLFQKYGIDNPDMNKLQFHLMLDEFF" + source 1814..2628 + /source="Exported" +ORIGIN + 1 tgctcgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcgg cgtccagcca tattcaacgg gaaacgtctt gctcgaggcc gcgattaaat + 1861 tccaacatgg atgctgattt atatgggtat aaatgggctc gcgataatgt cgggcaatca + 1921 ggtgcgacaa tctatcgatt gtatgggaag cccgatgcgc cagagttgtt tctgaaacat + 1981 ggcaaaggta gcgttgccaa tgatgttaca gatgagatgg tcagactaaa ctggctgacg + 2041 gaatttatgc ctcttccgac catcaagcat tttatccgta ctcctgatga tgcatggtta + 2101 ctcaccactg cgatccccgg gaaaacagca ttccaggtat tagaagaata tcctgattca + 2161 ggtgaaaata ttgttgatgc gctggcagtg ttcctgcgcc ggttgcattc gattcctgtt + 2221 tgtaattgtc cttttaacag cgatcgcgta tttcgtctgg ctcaggcgca atcacgaatg + 2281 aataacggtt tggttgatgc gagtgatttt gatgacgagc gtaatggctg gcctgttgaa + 2341 caagtctgga aagaaatgca taagcttttg ccattctcac cggattcagt cgtcactcat + 2401 ggtgatttct cacttgataa ccttattttt gacgagggga aattaatagg ttgtattgat + 2461 gttggacgag tcggaatcgc agaccgatac caggatcttg ccatcctatg gaactgcctc + 2521 ggtgagtttt ctccttcatt acagaaacgg ctttttcaaa aatatggtat tgataatcct + 2581 gatatgaata aattgcagtt tcatttgatg ctcgatgagt ttttctaa +// diff --git a/tools/create_assembly_picklists/test-data/emma_parts/p9_puror.gb b/tools/create_assembly_picklists/test-data/emma_parts/p9_puror.gb new file mode 100644 index 00000000..b0ebd6f9 --- /dev/null +++ b/tools/create_assembly_picklists/test-data/emma_parts/p9_puror.gb @@ -0,0 +1,90 @@ +LOCUS . 2415 bp DNA UNK 01-JAN-1980 +DEFINITION . +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature complement(6..11) + /note="BsmBI" + terminator 86..115 + /note="T3Te terminator" + /note="phage T3 early transcription terminator" + rep_origin 137..724 + /direction=RIGHT + /note="ori" + /note="high-copy-number ColE1/pMB1/pBR322/pUC origin of + replication" + terminator 736..763 + /note="T7Te terminator" + /note="phage T7 early transcription terminator" + source 5..1150 + /source="Exported" + promoter complement(1603..1705) + /note="cat promoter" + /note="promoter of the E. coli cat gene" + terminator 1706..1737 + /note="tonB terminator" + /note="bidirectional E. coli tonB-P14 transcription + terminator" + misc_feature 1803..1808 + /note="BsmBI" + source 1155..1809 + /source="Exported" + CDS 1816..2412 + /codon_start=1 + /gene="pac from Streptomyces" + /note="PuroR" + /note="confers resistance to puromycin" + /product="puromycin N-acetyltransferase" + /translation="TEYKPTVRLATRDDVPRAVRTLAAAFADYPATRHTVDPDRHIERV + TELQELFLTRVGLDIGKVWVADDGAAVAVWTTPESVEAGAVFAEIGPRMAELSGSRLAA + QQQMEGLLAPHRPKEPAWFLATVGVSPDHQGKGLGSAVVLPGVEAAERAGVPAFLETSA + PRNLPFYERLGFTVTADVECPKDRATWCMTRKPGA" + source 1814..2415 + /source="Exported" +ORIGIN + 1 tgctcgagac gaaaacgaat tcaagcttga tatcattcag gacgagcctc agactccagc + 61 gtaactggac tgcaatcaac tcactggctc accttcacgg gtgggccttt cttcggtaga + 121 aaatcaaagg atcttcttga gatccttttt ttctgcgcgt aatctgctgc ttgcaaacaa + 181 aaaaaccacc gctaccagcg gtggtttgtt tgccggatca agagctacca actctttttc + 241 cgaggtaact ggcttcagca gagcgcagat accaaatact gttcttctag tgtagccgta + 301 gttaggccac cacttcaaga actctgtagc accgcctaca tacctcgctc tgctaatcct + 361 gttaccagtg gctgctgcca gtggcgataa gtcgtgtctt accgggttgg actcaagacg + 421 atagttaccg gataaggcgc agcggtcggg ctgaacgggg ggttcgtgca cacagcccag + 481 cttggagcga acgacctaca ccgaactgag atacctacag cgtgagctat gagaaagcgc + 541 cacgcttccc gaagggagaa aggcggacag gtatccggta agcggcaggg tcggaacagg + 601 agagcgcacg agggagcttc cagggggaaa cgcctggtat ctttatagtc ctgtcgggtt + 661 tcgccacctc tgacttgagc atcgattttt gtgatgctcg tcaggggggc ggagcctatg + 721 gaaaaacgcc agcaacgcag aaaggcccac ccgaaggtga gccaggtgat tacatttggg + 781 ccctcattag aaaaactcat cgagcatcaa gtgaaactgc aatttattca tatcaggatt + 841 atcaatacca tatttttgaa aaagccgttt ctgtaatgaa ggagaaaact caccgaggca + 901 gttccatagg atggcaagat cctggtatcg gtctgcgatt ccgactcgtc caacatcaat + 961 acaacctatt aatttcccct cgtcaaaaat aaggttatca agtgagaaat caccatgagt + 1021 gacgactgaa tccggtgaga atggcaaaag cttatgcatt tctttccaga cttgttcaac + 1081 aggccagcca ttacgctcgt catcaaaatc actcgcacca accaaaccgt tattcattcg + 1141 tgattgcgcc tgagcgagac gaaatacgcg atcgccgtta aaaggacaat tacaaacagg + 1201 aatcgaatgc aaccggcgca ggaacactgc cagcgcatca acaatatttt cacctgaatc + 1261 aggatattct tctaatacct ggaatgctgt tttccctggg atcgcagtgg tgagtaacca + 1321 tgcatcatca ggagtacgga taaaatgctt gatggtcgga agaggcataa attccgtcag + 1381 ccagtttagc ctgaccatct catctgtaac atcattggca acgctacctt tgccatgttt + 1441 cagaaacaac tctggcgcat cgggcttccc atacaatcga tagattgtcg cacctgattg + 1501 cccgacatta tcgcgagccc atttataccc atataaatca gcatccatgt tggaatttaa + 1561 tcgcggcctc gagcaagacg tttcccgttg aatatggctc attttagctt ccttagctcc + 1621 tgaaaatctc gataactcaa aaaatacgcc cggtagtgat cttatttcat tatggtgaaa + 1681 gttggaacct cttacgtgcc gatcaagtca aaagcctccg gtcggaggct tttgactttc + 1741 tgctatggag gtcaggtatg atttaaatgg tcagtattga gcgatatcta gagaattcgt + 1801 cacgtctcgg cgtccaccga gtacaagccc acggtgcgcc tcgccacccg cgacgacgtc + 1861 cccagggccg tacgcaccct cgccgccgcg ttcgccgact accccgccac gcgccacacc + 1921 gtcgatccgg accgccacat cgagcgggtc accgagctgc aagaactctt cctcacgcgc + 1981 gtcgggctcg acatcggcaa ggtgtgggtc gcggacgacg gcgccgcggt ggcggtctgg + 2041 accacgccgg agagcgtcga agcgggggcg gtgttcgccg agatcggccc gcgcatggcc + 2101 gagttgagcg gttcccggct ggccgcgcag caacagatgg aaggcctcct ggcgccgcac + 2161 cggcccaagg agcccgcgtg gttcctggcc accgtcggcg tgtcgcccga ccaccagggc + 2221 aagggtctgg gcagcgccgt cgtgctcccc ggagtggagg cggccgagcg cgccggggtg + 2281 cccgccttcc tggaaacctc cgcgccccgc aacctcccct tctacgagcg gctcggcttc + 2341 accgtcaccg ccgacgtcga gtgcccgaag gaccgcgcga cctggtgcat gacccgcaag + 2401 cccggtgcct aataa +// diff --git a/tools/create_assembly_picklists/test-data/example_echo_plate.xlsx b/tools/create_assembly_picklists/test-data/example_echo_plate.xlsx new file mode 100644 index 0000000000000000000000000000000000000000..49f98d243f27cefdc04fcdfcf9510a6f4f5e0d37 GIT binary patch literal 12225 zcmbVS1yo#F(uUyf?j79SC4|NscX!v|L4yVel174C2-d;f2?Tc!t|5c~!QK95W_Mb>gv`rf)-_tyJfsVc(3Q-kn;*#s6QC>`MhHE%&>RDorkS&Fu_I^ 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This tricks the calculator into making - # a picklist with the desired ratio. - # For example, a part:backbone = 2:1 will multiply the - # backbone concentration by 2, therefore half as much of it will be - # added to the well. - quantities[part.replace(" ", "_")] = quantity * part_backbone_ratio - else: - quantities[part.replace(" ", "_")] = quantity + if backbone_name != '' and backbone_name != 'Non': + if part in backbone_name_list: + # This section multiplies the backbone concentration with the + # part:backbone molar ratio. This tricks the calculator into making + # a picklist with the desired ratio. + # For example, a part:backbone = 2:1 will multiply the + # backbone concentration by 2, therefore half as much of it will be + # added to the well. + quantities[part.replace(" ", "_")] = quantity * part_backbone_ratio + else: + quantities[part.replace(" ", "_")] = quantity source_plate.name = "Source" if destination_plate: diff --git a/tools/create_assembly_picklists/create_assembly_picklists.xml b/tools/create_assembly_picklists/create_assembly_picklists.xml index b06324b7..6f8f250b 100644 --- a/tools/create_assembly_picklists/create_assembly_picklists.xml +++ b/tools/create_assembly_picklists/create_assembly_picklists.xml @@ -38,8 +38,8 @@ --parts_files '$renamed_paths' --picklist '$picklist' --source_plate 'source_plate.xlsx' - --backbone_name '$backbone_name' - --part_backbone_ratio '$part_backbone_ratio' + --backbone_name '$adv.backbone_name' + --part_backbone_ratio '$adv.part_backbone_ratio' --quantity_unit '$quantity_unit' --part_quantity '$part_quantity' --buffer_volume '$buffer_volume' @@ -49,23 +49,25 @@ cp 'picklist.zip' '$output_zip' ]]> - + - - - - - + + + +

+ + +
@@ -171,8 +173,6 @@ - - @@ -193,6 +193,12 @@ create_assembly_picklists Provide a source plate map and an assembly plan, get a robotic picklist spreadsheet for Tecan EVO or Labcyte Echo. `Read more... `_ +**Advance parameter**: +--------------------- +* **Backbone Name(s)**: It can be one backbone or more than one (one name by line) +* **Backbone Molar Ratio**: between 0.0 and 1.0 +This section is to multiplie the backbone concentration with the part:backbone molar ratio. This tricks the calculator into making a picklist with the desired ratio. For example, a part:backbone = 2:1 will multiply the backbone concentration by 2, therefore half as much of it will be added to the well. +**If Part quantity unit is ng**: Backbone Molar Ratio calculation is not performed in this case. ]]> From 3207cadfe51a147ade7b163bdd661f95950540b0 Mon Sep 17 00:00:00 2001 From: ramiz khaled Date: Mon, 11 Aug 2025 15:27:01 +0200 Subject: [PATCH 3/7] fix: json data --- tools/parameters_maystro/maystro.py | 98 +++++++++++++++++++ .../parameters_maystro/maystro_workflow_1.xml | 25 ++++- .../test-data/test-JSON_workflow1.json | 4 + 3 files changed, 124 insertions(+), 3 deletions(-) create mode 100644 tools/parameters_maystro/maystro.py diff --git a/tools/parameters_maystro/maystro.py b/tools/parameters_maystro/maystro.py new file mode 100644 index 00000000..3736caf6 --- /dev/null +++ b/tools/parameters_maystro/maystro.py @@ -0,0 +1,98 @@ +import argparse +import tempfile +import os +import json +import shutil + + +def parse_command_line_args(): + parser = argparse.ArgumentParser(description="Maystro JSON Handler") + + parser.add_argument("--distribute_json", required=True, help="true or false") + parser.add_argument("--json_from_workflow", required=False, nargs='+', help="JSON files from tools", default=[]) + parser.add_argument("--json_from_user", required=False, help="User-provided JSON") + parser.add_argument("--json_name_mapping", required=True, help="map the real json name") + parser.add_argument("--output_workflow", required=True, help="JSON output for next workflow steps") + parser.add_argument("--output_user", required=True, help="Final JSON output to user") + + return parser.parse_args() + + +def parse_file_name_mapping(mapping_str): + mapping = {} + if mapping_str: + for pair in mapping_str.split(','): + stored, original = pair.strip().split(':', 1) + # Strip .json from original + real_name = os.path.splitext(original)[0] + mapping[os.path.basename(stored)] = real_name + return mapping + + +def handle_distribute_json_false(args): + temp_dir = tempfile.mkdtemp(prefix="maystro_merge_") + print(f"[INFO] Watching temp dir for new JSONs: {temp_dir}") + + try: + # Collect JSONs from json_from_workflow + initial_jsons = list(filter(os.path.isfile, args.json_from_workflow)) + print(f"[INFO] Initial JSONs from workflow: {initial_jsons}") + + # Parse filename mapping if provided + filename_mapping = parse_file_name_mapping(getattr(args, 'json_name_mapping', '')) + + # Merge all together + merged = {} + for file_path in initial_jsons: + try: + with open(file_path, 'r') as f: + data = json.load(f) + basename = os.path.basename(file_path) + real_name = filename_mapping.get(basename, basename) # fallback if not in mapping + merged[real_name] = data + print(f"[INFO] Added data under key: {real_name}") + except json.JSONDecodeError as e: + print(f"[WARN] Skipping invalid JSON file {file_path}: {e}") + + with open(args.output_user, "w") as f: + json.dump(merged, f, indent=2) + print(f"[INFO] Merged JSON written to: {args.output_user}") + + finally: + print(f"[INFO] Cleaning up: {temp_dir}") + shutil.rmtree(temp_dir) + + +def merge_json_files(paths): + merged = {} + for path in paths: + try: + with open(path, "r") as f: + data = json.load(f) + merged.update(data) + except Exception as e: + print(f"[WARN] Skipping {path}: {e}") + return merged + + +def handle_distribute_json_true(args): + if not args.json_from_user: + raise ValueError("json_from_user is required when distribute_json is true") + + with open(args.json_from_user, 'r') as in_f: + user_data = json.load(in_f) + + with open(args.output_workflow, 'w') as out_f: + json.dump(user_data, out_f, indent=2) + + +def main(): + args = parse_command_line_args() + + if args.distribute_json.lower() == 'false': + handle_distribute_json_false(args) + else: + handle_distribute_json_true(args) + +if __name__ == "__main__": + main() diff --git a/tools/parameters_maystro/maystro_workflow_1.xml b/tools/parameters_maystro/maystro_workflow_1.xml index adf0cc62..6b6531c7 100644 --- a/tools/parameters_maystro/maystro_workflow_1.xml +++ b/tools/parameters_maystro/maystro_workflow_1.xml @@ -8,6 +8,10 @@ cp '$user_json' '$output_json' #else python3 -c "import json; params = { + 'avoid_patterns': '$avoid_patterns', + 'hairpin_constraints': '$hairpin_constraints', + 'gc_constraints': '$gc_constraints', + 'kmer_size': '$kmer_size', 'assembly_plan_name': '$assembly_plan_name', 'topology': '$topology', 'enzyme': '$enzyme', @@ -22,6 +26,10 @@ && echo DEBG && cat '$output_json' ]]> + + + + @@ -47,7 +55,18 @@ - + + + + + @@ -59,7 +78,7 @@ - + @@ -68,7 +87,7 @@ - + diff --git a/tools/parameters_maystro/test-data/test-JSON_workflow1.json b/tools/parameters_maystro/test-data/test-JSON_workflow1.json index 44e815d4..51433ad9 100644 --- a/tools/parameters_maystro/test-data/test-JSON_workflow1.json +++ b/tools/parameters_maystro/test-data/test-JSON_workflow1.json @@ -1,4 +1,8 @@ { + "avoid_patterns": "BsaI_site\nBsmBI_site\nBbsI_site\nSapI_site\n8x1mer\n5x3mer\n9x2mer", + "hairpin_constraints": "stem_size=20, hairpin_window=200", + "gc_constraints": "mini=0.1, maxi=0.9, window=100\nmini=0.3, maxi=0.7, window=100", + "kmer_size": "15", "execution": "true", "db_uri": "postgresql://postgres:RK17@localhost:5432/test_fragments_db", "table": "sample", From 767392e3136912fa30d1e0786eba789dd77d722c Mon Sep 17 00:00:00 2001 From: ramiz khaled Date: Mon, 11 Aug 2025 15:33:23 +0200 Subject: [PATCH 4/7] update: evaluate_manuf:0.3.0+2 --- .../evaluate_manufacturability.py | 148 ++++++- .../evaluate_manufacturability.xml | 414 ++++++++++++++++-- .../DB_genbank_simulation/p16_bGHpolyA.gb | 24 + .../DB_genbank_simulation/p19_mNeoGreen.gb | 44 ++ .../DB_genbank_simulation/p3_2_CAG.gb | 33 ++ .../test-data/NO_missing.txt | 1 + .../test-data/manufacturability_report.tsv | 11 + .../test-data/missing.txt | 11 + 8 files changed, 634 insertions(+), 52 deletions(-) create mode 100644 tools/evaluate_manufacturability/test-data/DB_genbank_simulation/p16_bGHpolyA.gb create mode 100644 tools/evaluate_manufacturability/test-data/DB_genbank_simulation/p19_mNeoGreen.gb create mode 100644 tools/evaluate_manufacturability/test-data/DB_genbank_simulation/p3_2_CAG.gb create mode 100644 tools/evaluate_manufacturability/test-data/NO_missing.txt create mode 100644 tools/evaluate_manufacturability/test-data/manufacturability_report.tsv create mode 100644 tools/evaluate_manufacturability/test-data/missing.txt diff --git a/tools/evaluate_manufacturability/evaluate_manufacturability.py b/tools/evaluate_manufacturability/evaluate_manufacturability.py index 65607343..30501f1b 100644 --- a/tools/evaluate_manufacturability/evaluate_manufacturability.py +++ b/tools/evaluate_manufacturability/evaluate_manufacturability.py @@ -44,14 +44,14 @@ def evaluate_manufacturability(files_to_evaluate, file_name_mapping, output_tsv, folder=None, use_file_names_as_ids=use_file_names_as_id ) - # #try: - # #if not records_to_evaluate: - # #print('records to evaluate: is empty') - # #else: - # #for record in records_to_evaluate: - # #print(f'records to evaluate: {record}') - # #except Exception as e: - # #print(f'An error occurred: {e}') + # try: + # if not records_to_evaluate: + # print('records to evaluate: is empty') + # else: + # for record in records_to_evaluate: + # print(f'records to evaluate: {record}') + # except Exception as e: + # print(f'An error occurred: {e}') length_cutoff = 100 for part in records_to_evaluate: @@ -117,7 +117,7 @@ def evaluate_manufacturability(files_to_evaluate, file_name_mapping, output_tsv, except ValueError: print(f"Skipping invalid k-mer size: {k_size}") - print(f'constraint_list is{constraint_list}') + # print(f'constraint_list is{constraint_list}') # constraint_list apply dataframe = cr.constraints_breaches_dataframe(constraint_list, records_to_evaluate) @@ -190,10 +190,12 @@ def evaluate_manufacturability(files_to_evaluate, file_name_mapping, output_tsv, def parse_command_line_args(): parser = argparse.ArgumentParser(description="Evaluate manufacturability of DNA sequences.") - parser.add_argument("--files_to_evaluate", required=True, + parser.add_argument("--files_to_evaluate", required=False, help="List of GenBank files (Comma-separated)") parser.add_argument('--file_name_mapping', type=str, help='Mapping of Galaxy filenames to original filenames') + parser.add_argument('--DB_file_name_mapping', type=str, + help='Mapping of Galaxy filenames to original DB filenames') parser.add_argument("--output_tsv", required=True, help="Excel file name") parser.add_argument("--output_pdf", required=True, help="PDF file name") parser.add_argument("--outdir_gb", required=True, help="DIR for annotated GenBank files") @@ -211,6 +213,13 @@ def parse_command_line_args(): help="JSON params for the tool") parser.add_argument("--use_json_param", required=True, help="If use JSON as param source") + parser.add_argument("--mode", required=True, + help="mode d'utilisation: standard ou workflow") + parser.add_argument("--DB_report", required=False, + help="In wkf mode") + parser.add_argument("--DB_genbank_files", required=False, + help="IN wkf mode") + return parser.parse_args() @@ -268,6 +277,74 @@ def split_lines(val): args = parse_command_line_args() + ### + if "--mode" in sys.argv: + mode_index = sys.argv.index("--mode") + 1 + mode = sys.argv[mode_index].strip() + + skip_evaluation = False + use_DB_files = False + DB_genbank_files = [] + + if mode == "wkf": + + if "--DB_report" not in sys.argv: + print("ERROR: --DB_report is required in wkf mode.") + sys.exit(1) + db_index = sys.argv.index("--DB_report") + 1 + db_report_path = sys.argv[db_index] + + if "--DB_genbank_files" in sys.argv: + db_gb_index = sys.argv.index("--DB_genbank_files") + 1 + DB_genbank_files = sys.argv[db_gb_index].split(",") + else: + DB_genbank_files = [] + + if not os.path.isfile(db_report_path): + print(f"ERROR: DB report file not found at {db_report_path}") + sys.exit(1) + + with open(db_report_path, 'r') as f: + lines = [line.strip() for line in f.readlines() if line.strip()] + + if not lines: + print("ERROR: DB_report file is empty.") + sys.exit(1) + + header = lines[0] + if header.startswith("Missing fragment in DB:"): + + missing_fragments = lines[1:] + + # Parse file_name_mapping + if isinstance(args.file_name_mapping, str): + mapping_dict = dict(item.split(":") for item in args.file_name_mapping.split(",")) + else: + mapping_dict = {} + + # Logical names + provided_filenames = [os.path.splitext(v)[0] for v in mapping_dict.values()] + + # print(f'provided_filenames is : {provided_filenames}') + + unmatched = [ + frag for frag in missing_fragments + if os.path.splitext(frag)[0] not in provided_filenames + ] + + if unmatched: + print(f"ERROR: The following missing fragment(s) must be provided as .gb files: {', '.join(unmatched)}") + sys.exit(1) + else: + use_DB_files = True # Append after evaluation + + elif header.startswith("NO missing fragments in DB"): + skip_evaluation = True + else: + print(f"ERROR: Invalid header in DB_report: '{header}'") + sys.exit(1) + ### + # Default values from command-line avoid_patterns, hairpin_constraints, gc_constraints, kmer_size = extract_constraints_from_args(args) @@ -304,10 +381,47 @@ def split_lines(val): "kmer_size": kmer_size } - evaluate_manufacturability( - params["files_to_evaluate"], params["file_name_mapping"], - params["output_tsv"], params["output_pdf"], params["outdir_gb"], - params["use_file_names_as_id"], params["avoid_patterns"], - params["hairpin_constraints"], params["gc_constraints"], - params["kmer_size"] - ) + if not skip_evaluation: + evaluate_manufacturability( + params["files_to_evaluate"], params["file_name_mapping"], + params["output_tsv"], params["output_pdf"], params["outdir_gb"], + params["use_file_names_as_id"], params["avoid_patterns"], + params["hairpin_constraints"], params["gc_constraints"], + params["kmer_size"] + ) + + if mode == "wkf" and (skip_evaluation or use_DB_files): + if DB_genbank_files: + print(f"DB_genbank_files is: {DB_genbank_files}") + print("Adding DB GenBank files to output collection using DB_file_name_mapping...") + + os.makedirs(params["outdir_gb"], exist_ok=True) + + # mapping real DB gb file name + if isinstance(args.DB_file_name_mapping, str): + print (f'DB_file_name_mapping is: {args.DB_file_name_mapping}') + DB_mapping_dict = dict(item.split(":") for item in args.DB_file_name_mapping.split(",")) + else: + DB_mapping_dict={} + + for path in DB_genbank_files: + basename = os.path.basename(path) + logical_name = DB_mapping_dict.get(path) or DB_mapping_dict.get(basename) + + if not logical_name: + print(f"WARNING: No mapping found for DB GenBank file: {path}. Skipping.") + continue + + output_filename = os.path.splitext(logical_name)[0] + ".gb" + dest_path = os.path.join(params["outdir_gb"], output_filename) + + try: + with open(path, 'r') as src, open(dest_path, 'w') as dst: + dst.write(src.read()) + print(f"Copied and renamed: {path} → {dest_path}") + except Exception as e: + print(f"ERROR: Failed to copy {path} → {dest_path}: {e}") + else: + print("No DB GenBank files to append, continuing without error.") + + diff --git a/tools/evaluate_manufacturability/evaluate_manufacturability.xml b/tools/evaluate_manufacturability/evaluate_manufacturability.xml index a5e37443..1e39512e 100644 --- a/tools/evaluate_manufacturability/evaluate_manufacturability.xml +++ b/tools/evaluate_manufacturability/evaluate_manufacturability.xml @@ -1,8 +1,8 @@ Evaluate DNA manufacturability with customizable constraints - 1 - 0.2.0 + 2 + 0.3.0 flametree @@ -16,8 +16,22 @@ openpyxl - + + + + + + + + + + + + + + @@ -85,20 +122,7 @@ impossible to run it in conda env with this comand because there is a step to extract the the file name in galaxy (.dat) in line 83 of the python code--> - - - - - - - - - - - - - - + @@ -118,6 +142,23 @@ + + + + + + + + + + + + + + + + + @@ -125,7 +166,7 @@ - + @@ -186,26 +227,189 @@ - - - - - - - - - - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -220,6 +424,113 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -270,6 +581,21 @@ + + + + + + + + + + + + + + + @@ -281,6 +607,10 @@ Get plots of patterns impacting synthesis and assembly difficulty deppanding on **Parameters**: --------------- +* **Mode**: + This option allows you to choose the mode in which the tool will be executed: + - Standard: Runs the tool as a standalone application. + - Workflow: Adds additional options to make the tool more flexible and interactive within a workflow. * **GenBank File(s)**: List of GenBank files to be processed. * **Use parameter from a JSON file**: Yes/No parameter to indicate if user want to set parameter manually or using a json file @@ -300,6 +630,20 @@ Get plots of patterns impacting synthesis and assembly difficulty deppanding on In case on using more than one combination, each one msut be on a ligne. * **K-mer Uniqueness Size**: Avoid sub-sequence of length k with homologies elsewhere. * **Use File Names As Sequence IDs**: Recommended if the GenBank file names represent the fragment names. + +**DEMO ** +---------- + + Executes the tool in standard mode using default parameters tailored to the test dataset. + + To start a demo you need to download the test dataset and the defaulte parameter aapted: + + - **GenBank File(s):** `Download GenBank files `_ + + **Note:** Make GenBank files as a collection list. + `How to make collection `_ + + - **Default Parameters:** Thy are provided `here `_ as JSON file (Enabel the Use parameter from a JSON file option) ]]> diff --git a/tools/evaluate_manufacturability/test-data/DB_genbank_simulation/p16_bGHpolyA.gb b/tools/evaluate_manufacturability/test-data/DB_genbank_simulation/p16_bGHpolyA.gb new file mode 100644 index 00000000..f4e400b3 --- /dev/null +++ b/tools/evaluate_manufacturability/test-data/DB_genbank_simulation/p16_bGHpolyA.gb @@ -0,0 +1,24 @@ +LOCUS . 257 bp DNA UNK 01-JAN-1980 +DEFINITION .. +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + polyA_signal 33..257 + /note="bGH poly(A) signal" + /note="bovine growth hormone polyadenylation signal" + source 1..257 + /source="Exported" + misc_feature 1..257 + /source="p16_bGHpolyA" + /note="From p16_bGHpolyA" +ORIGIN + 1 ctctggggtt cgaaatgacc gaccaagcga cgctgtgcct tctagttgcc agccatctgt + 61 tgtttgcccc tcccccgtgc cttccttgac cctggaaggt gccactccca ctgtcctttc + 121 ctaataaaat gaggaaattg catcgcattg tctgagtagg tgtcattcta ttctgggggg + 181 tggggtgggg caggacagca agggggagga ttgggaagac aatagcaggc atgctgggga + 241 tgcggtgggc tctatgg +// diff --git a/tools/evaluate_manufacturability/test-data/DB_genbank_simulation/p19_mNeoGreen.gb b/tools/evaluate_manufacturability/test-data/DB_genbank_simulation/p19_mNeoGreen.gb new file mode 100644 index 00000000..515c6c7c --- /dev/null +++ b/tools/evaluate_manufacturability/test-data/DB_genbank_simulation/p19_mNeoGreen.gb @@ -0,0 +1,44 @@ +LOCUS . 716 bp DNA UNK 01-JAN-1980 +DEFINITION .. +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + misc_feature 1..11 + /note="KozaK" + CDS 9..11 + /codon_start=1 + /note="ATG" + /translation="M" + CDS 12..716 + /codon_start=1 + /note="mNeonGreen" + /product="bright monomeric yellow-green fluorescent protein + derived from LanYFP (Shaner et al., 2013)" + /translation="VSKGEEDNMASLPATHELHIFGSINGVDFDMVGQGTGNPNDGYEE + LNLKSTKGDLQFSPWILVPHIGYGFHQYLPYPDGMSPFQAAMVDGSGYQVHRTMQFEDG + ASLTVNYRYTYEGSHIKGEAQVKGTGFPADGPVMTNSLTAADWCRSKKTYPNDKTIIST + FKWSYTTGNGKRYRSTARTTYTFAKPMAANYLKNQPMYVFRKTELKHSKTELNFKEWQK + AFTDVMGMDELYK" + source 1..716 + /source="Exported" + misc_feature 1..716 + /source="p19_mNeoGreen" + /note="From p19_mNeoGreen" +ORIGIN + 1 ccgccaccat ggtgagcaag ggcgaggagg ataacatggc ctctctccca gcgacacatg + 61 agttacacat ctttggctcc atcaacggtg tggactttga catggtgggt cagggcaccg + 121 gcaatccaaa tgatggttat gaggagttaa acctgaagtc caccaagggt gacctccagt + 181 tctccccctg gattctggtc cctcatatcg ggtatggctt ccatcagtac ctgccctacc + 241 ctgacgggat gtcgcctttc caggccgcca tggtagatgg ctccggatac caagtccatc + 301 gcacaatgca gtttgaagat ggtgcctccc ttactgttaa ctaccgctac acctacgagg + 361 gaagccacat caaaggagag gcccaggtga aggggactgg tttccctgct gacggtcctg + 421 tgatgaccaa ctcgctgacc gctgcggact ggtgcaggtc gaagaagact taccccaacg + 481 acaaaaccat catcagtacc tttaagtgga gttacaccac tggaaatggc aagcgctacc + 541 ggagcactgc gcggaccacc tacacctttg ccaagccaat ggcggctaac tatctgaaga + 601 accagccgat gtacgtgttc cgtaagacgg agctcaagca ctccaagacc gagctcaact + 661 tcaaggagtg gcaaaaggcc tttaccgatg tgatgggcat ggacgagctg tacaag +// diff --git a/tools/evaluate_manufacturability/test-data/DB_genbank_simulation/p3_2_CAG.gb b/tools/evaluate_manufacturability/test-data/DB_genbank_simulation/p3_2_CAG.gb new file mode 100644 index 00000000..e50c16fb --- /dev/null +++ b/tools/evaluate_manufacturability/test-data/DB_genbank_simulation/p3_2_CAG.gb @@ -0,0 +1,33 @@ +LOCUS . 690 bp DNA UNK 01-JAN-1980 +DEFINITION .. +ACCESSION +VERSION +KEYWORDS . +SOURCE . + ORGANISM . + . +FEATURES Location/Qualifiers + enhancer 19..398 + /note="CMV enhancer" + /note="human cytomegalovirus immediate early enhancer" + promoter 400..675 + /note="chicken beta-actin promoter" + source 1..690 + /source="Exported" + misc_feature 1..690 + /source="p3_2_CAG" + /note="From p3_2_CAG" +ORIGIN + 1 ggatctgata tcatcgtcga cattgattat tgactagtta ttaatagtaa tcaattacgg + 61 ggtcattagt tcatagccca tatatggagt tccgcgttac ataacttacg gtaaatggcc + 121 cgcctggctg accgcccaac gacccccgcc cattgacgtc aataatgacg tatgttccca + 181 tagtaacgcc aatagggact ttccattgac gtcaatgggt ggactattta cggtaaactg + 241 cccacttggc agtacatcaa gtgtatcata tgccaagtac gccccctatt gacgtcaatg + 301 acggtaaatg gcccgcctgg cattatgccc agtacatgac cttatgggac tttcctactt + 361 ggcagtacat ctacgtatta gtcatcgcta ttaccatggt cgaggtgagc cccacgttct + 421 gcttcactct ccccatctcc cccccctccc cacccccaat tttgtattta tttatttttt + 481 aattattttg tgcagcgatg ggggcggggg gggggggggc gcgcgccagg cggggcgggg + 541 cggggcgagg ggcggggcgg ggcgaggcgg agaggtgcgg cggcagccaa tcagagcggc + 601 gcgctccgaa agtttccttt tatggcgagg cggcggcggc ggcggcccta taaaaagcga + 661 agcgcgcggc gggcgggagt cgctgcgttg +// diff --git a/tools/evaluate_manufacturability/test-data/NO_missing.txt b/tools/evaluate_manufacturability/test-data/NO_missing.txt new file mode 100644 index 00000000..c9bdf1c7 --- /dev/null +++ b/tools/evaluate_manufacturability/test-data/NO_missing.txt @@ -0,0 +1 @@ +NO missing fragments in DB \ No newline at end of file diff --git a/tools/evaluate_manufacturability/test-data/manufacturability_report.tsv b/tools/evaluate_manufacturability/test-data/manufacturability_report.tsv new file mode 100644 index 00000000..10a483df --- /dev/null +++ b/tools/evaluate_manufacturability/test-data/manufacturability_report.tsv @@ -0,0 +1,11 @@ +sequence BsaI BsmBI BbsI SapI 8-repeats 1-mers 5-repeats 3-mers 9-repeats 2-mers 20-160-20bp hairpin GC outside 30-70%/100bp GC outside 10-90%/100bp 15bp homologies +p8_Linker1 5-11(-), 1155-1161(-), 1802-1808(+) 97-112, 738-753, 1704-1720, 1722-1738 +p9_PuroR 5-11(-), 1155-1161(-), 1802-1808(+) 1789-2405 97-112, 738-753, 1704-1720, 1722-1738 +p9_mTagBFP2 5-11(-), 1155-1161(-), 1802-1808(+) 2112-2118(+) 1827-1834(-) 97-112, 738-753, 1704-1720, 1722-1738 +p4_Kt-L7Ae-Weiss 1142-1148(+), 1190-1196(-), 1838-1844(+) 1195-1201(+) 401-416, 1042-1057, 1261-1277, 1279-1295 +p6_Nt-IgKLsequence 1142-1148(+), 1231-1237(-), 1879-1885(+) 1236-1242(+) 401-416, 1042-1057, 1302-1318, 1320-1336 +HC_Amp_ccdB 677-683(+) 72-78(-), 942-948(+) 891-925, 1022-1037, 1038-1053, 1674-1706 +p15_PuroR 1142-1148(+), 1769-1775(-), 2417-2423(+) 1774-1780(+) 1136-1754 401-416, 1042-1057, 1840-1856, 1858-1874 +p9_BSDR 5-11(-), 1155-1161(-), 1802-1808(+) 1890-1896(+) 2060-2208 97-112, 738-753, 1704-1720, 1722-1738 +p6_Kozak-ATG 1142-1148(+), 1201-1207(-), 1849-1855(+) 1206-1212(+) 401-416, 1042-1057, 1272-1288, 1290-1306 +p7_L7Ae-Weiss 1142-1148(+), 1514-1520(-), 2162-2168(+) 1519-1525(+) 401-416, 1042-1057, 1585-1601, 1603-1619 diff --git a/tools/evaluate_manufacturability/test-data/missing.txt b/tools/evaluate_manufacturability/test-data/missing.txt new file mode 100644 index 00000000..5e77b3ed --- /dev/null +++ b/tools/evaluate_manufacturability/test-data/missing.txt @@ -0,0 +1,11 @@ +Missing fragment in DB: +p15_PuroR +p9_PuroR +p9_mTagBFP2 +p9_BSDR +p8_Linker1 +p7_L7Ae-Weiss +p6_Nt-IgKLsequence +p6_Kozak-ATG +p4_Kt-L7Ae-Weiss +HC_Amp_ccdB From 6a3e2c1db3e0bd94cb58e6ba86da2b2790ba37e6 Mon Sep 17 00:00:00 2001 From: ramiz khaled Date: Fri, 5 Sep 2025 11:10:58 +0200 Subject: [PATCH 5/7] update: evaluate_manufacturability and seq_from_db: inteaction with report missing parts --- .../evaluate_manufacturability.py | 15 +-- .../evaluate_manufacturability.xml | 1 + .../test-data/NO_missing.txt | 1 - .../test-data/missing.txt | 7 -- tools/seq_from_db/get_db_info.py | 38 ++++--- tools/seq_from_db/seq_form_db.xml | 101 +++++++++++++++++- .../test-data/test_missing_input.csv | 12 ++- 7 files changed, 134 insertions(+), 41 deletions(-) diff --git a/tools/evaluate_manufacturability/evaluate_manufacturability.py b/tools/evaluate_manufacturability/evaluate_manufacturability.py index 30501f1b..bc5723a8 100644 --- a/tools/evaluate_manufacturability/evaluate_manufacturability.py +++ b/tools/evaluate_manufacturability/evaluate_manufacturability.py @@ -308,13 +308,11 @@ def split_lines(val): lines = [line.strip() for line in f.readlines() if line.strip()] if not lines: - print("ERROR: DB_report file is empty.") - sys.exit(1) - - header = lines[0] - if header.startswith("Missing fragment in DB:"): + skip_evaluation = True + + else: - missing_fragments = lines[1:] + missing_fragments = lines[0:] # Parse file_name_mapping if isinstance(args.file_name_mapping, str): @@ -338,11 +336,6 @@ def split_lines(val): else: use_DB_files = True # Append after evaluation - elif header.startswith("NO missing fragments in DB"): - skip_evaluation = True - else: - print(f"ERROR: Invalid header in DB_report: '{header}'") - sys.exit(1) ### # Default values from command-line diff --git a/tools/evaluate_manufacturability/evaluate_manufacturability.xml b/tools/evaluate_manufacturability/evaluate_manufacturability.xml index 1e39512e..e9f2585d 100644 --- a/tools/evaluate_manufacturability/evaluate_manufacturability.xml +++ b/tools/evaluate_manufacturability/evaluate_manufacturability.xml @@ -397,6 +397,7 @@ + diff --git a/tools/evaluate_manufacturability/test-data/NO_missing.txt b/tools/evaluate_manufacturability/test-data/NO_missing.txt index c9bdf1c7..e69de29b 100644 --- a/tools/evaluate_manufacturability/test-data/NO_missing.txt +++ b/tools/evaluate_manufacturability/test-data/NO_missing.txt @@ -1 +0,0 @@ -NO missing fragments in DB \ No newline at end of file diff --git a/tools/evaluate_manufacturability/test-data/missing.txt b/tools/evaluate_manufacturability/test-data/missing.txt index 5e77b3ed..f29e6e1f 100644 --- a/tools/evaluate_manufacturability/test-data/missing.txt +++ b/tools/evaluate_manufacturability/test-data/missing.txt @@ -1,10 +1,3 @@ -Missing fragment in DB: -p15_PuroR -p9_PuroR -p9_mTagBFP2 -p9_BSDR -p8_Linker1 -p7_L7Ae-Weiss p6_Nt-IgKLsequence p6_Kozak-ATG p4_Kt-L7Ae-Weiss diff --git a/tools/seq_from_db/get_db_info.py b/tools/seq_from_db/get_db_info.py index 5c4035a0..648a7f94 100644 --- a/tools/seq_from_db/get_db_info.py +++ b/tools/seq_from_db/get_db_info.py @@ -93,7 +93,7 @@ def wait_for_db(uri, timeout=60): raise Exception("Database connection failed after timeout.") -def fetch_annotations(csv_file, sequence_column, annotation_columns, db_uri, table_name, fragment_column_name, output): +def fetch_annotations(csv_file, sequence_column, annotation_columns, db_uri, table_name, fragment_column_name, output, output_report): """Fetch annotations from the database and save the result as GenBank files.""" db_uri = fix_db_uri(db_uri) df = pd.read_csv(csv_file, sep=',', header=None) @@ -130,10 +130,14 @@ def fetch_annotations(csv_file, sequence_column, annotation_columns, db_uri, tab db_fragments = set(fragment_map.keys()) missing_fragments = sorted(list(csv_fragments - db_fragments)) - if missing_fragments: - raise ValueError( - f" Missing fragments in DB: {', '.join(missing_fragments)}" - ) + + # Write report file + with open(output_report, "w") as report_file: + if missing_fragments: + for frag in missing_fragments: + report_file.write(f"{frag}\n") + else: + report_file.write("") # === CONTINUE WITH GB FILE CREATION === for _, row in df.iterrows(): @@ -164,8 +168,14 @@ def fetch_annotations(csv_file, sequence_column, annotation_columns, db_uri, tab try: for annotated_row in annotated_data: backbone_id = annotated_row["Backbone"] + for fragment in annotated_row["Fragments"]: fragment_id = fragment["id"] + + # Skip generation for missing fragments + if fragment_id in missing_fragments: + continue + sequence = fragment.get(sequence_column, "") annotation = fragment.get(annotation_columns, "") @@ -182,7 +192,7 @@ def fetch_annotations(csv_file, sequence_column, annotation_columns, db_uri, tab k: str(fragment[k]) for k in annotation_columns if k in fragment } - # LOCUS line extraction from annotation (copy-paste the LOCUS from annotation) + # LOCUS line extraction from annotation locus_line_match = re.search(r"LOCUS\s+.+", annotation) if locus_line_match: locus_line = locus_line_match.group() @@ -190,41 +200,36 @@ def fetch_annotations(csv_file, sequence_column, annotation_columns, db_uri, tab print(f"LOCUS info missing for fragment {fragment_id}") locus_line = f"LOCUS {fragment_id: <20} {len(sequence)} bp DNA linear UNK 01-JAN-2025" - # Format sequence as per GenBank standards (with ORIGIN and line breaks) + # Format sequence if "ORIGIN" in sequence: origin_block = sequence.strip() else: - # Format sequence as per GenBank standards (with ORIGIN and line breaks) formatted_sequence = "ORIGIN\n" seq_str = str(record.seq) - for i in range(0, len(seq_str), 60): # 60 bases per line + for i in range(0, len(seq_str), 60): line_seq = seq_str[i:i + 60] formatted_sequence += f"{str(i + 1).rjust(9)} { ' '.join([line_seq[j:j+10] for j in range(0, len(line_seq), 10)]) }\n" origin_block = formatted_sequence.strip() - # Find and copy the FEATURES section directly from annotation + # Extract FEATURES section features_section = "" features_start = annotation.find("FEATURES") if features_start != -1: features_section = annotation[features_start:] - # Writing the GenBank file + # Write GenBank file if not os.path.exists(output): os.makedirs(output) gb_filename = os.path.join(output, f"{fragment_id}.gb") with open(gb_filename, "w") as f: - # Write the LOCUS line f.write(locus_line + "\n") - # Write DEFINITION, ACCESSION, and other annotations f.write(f"DEFINITION {record.description}\n") f.write(f"ACCESSION {record.id}\n") f.write(f"VERSION DB\n") f.write(f"KEYWORDS .\n") f.write(f"SOURCE .\n") - # Write the FEATURES section directly from annotation f.write(features_section) - # Write the ORIGIN section f.write(origin_block + "\n") f.write("//\n") @@ -244,6 +249,7 @@ def main(): parser.add_argument("--fragment_column", required=False, help="Fragment column name in the database") parser.add_argument("--output", required=True, help="Output dir for gb files") parser.add_argument("--json_conf", required=False, help="JSON config file with DB parameters") + parser.add_argument("--report", required=True, help="Output report for fragments checking in DB") args = parser.parse_args() # get param and chek for json @@ -287,7 +293,7 @@ def main(): time.sleep(2) # Fetch annotations from the database and save as gb - fetch_annotations(args.input, sequence_column, annotation_column, db_uri, table, fragment_column, args.output) + fetch_annotations(args.input, sequence_column, annotation_column, db_uri, table, fragment_column, args.output, args.report) if __name__ == "__main__": main() diff --git a/tools/seq_from_db/seq_form_db.xml b/tools/seq_from_db/seq_form_db.xml index 43e5621c..b8ffe5d4 100644 --- a/tools/seq_from_db/seq_form_db.xml +++ b/tools/seq_from_db/seq_form_db.xml @@ -1,8 +1,8 @@ Import fragment's data from an accessible DB and export it as .gb files - 1 - 0.2.0 + 2 + 0.3.0 pandas @@ -25,6 +25,7 @@ --json_conf '$json_use.json_conf' #end if --output 'outdir' + --report '$report' ]]> @@ -46,6 +47,7 @@ + @@ -121,6 +123,11 @@ + + + + + @@ -191,6 +198,96 @@ + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + diff --git a/tools/seq_from_db/test-data/test_missing_input.csv b/tools/seq_from_db/test-data/test_missing_input.csv index 559fbfb3..9893c378 100644 --- a/tools/seq_from_db/test-data/test_missing_input.csv +++ b/tools/seq_from_db/test-data/test_missing_input.csv @@ -1,4 +1,8 @@ -Sample-1,ACP10001AaCbbBS,NEW20001BbDccKT,XYZ10003AaCbbBS -Sample-2,CFP10002AaCbbBS,ACP10001AaCbbBS,ALT30005CcEddLM -Sample-3,XYZ10003AaCbbBS,ALT30005CcEddLM,ACP10001AaCbbBS -Sample-4,QWE10004AaCbbBS,NEW20001BbDccKT,CFP10002AaCbbBS +Sample-1,ACP10001AaCbbBS,NEW20001BbDccKT,XYZ10003AaCbbBS,,, +Sample-2,CFP10002AaCbbBS,ACP10001AaCbbBS,ALT30005CcEddLM,,, +Sample-3,XYZ10003AaCbbBS,ALT30005CcEddLM,ACP10001AaCbbBS,,, +Sample-4,QWE10004AaCbbBS,NEW20001BbDccKT,CFP10002AaCbbBS,,, +construct_3,construct_1,part_L,part_J,part_K,, +construct_4,construct_2,part_L,part_J,part_K,, +construct_1,part_A,part_B,part_C,part_D,part_E,part_F +construct_2,part_A,part_G,part_H,part_I,part_F, From 4156e7f4aba04b66d415a936e4cfd0906a735997 Mon Sep 17 00:00:00 2001 From: ramiz khaled Date: Fri, 5 Sep 2025 11:15:57 +0200 Subject: [PATCH 6/7] fix: parameters fixing --- tools/parameters_maystro/test-data/test_json_workflow2.json | 3 ++- 1 file changed, 2 insertions(+), 1 deletion(-) diff --git a/tools/parameters_maystro/test-data/test_json_workflow2.json b/tools/parameters_maystro/test-data/test_json_workflow2.json index a2939a9e..0a72377c 100644 --- a/tools/parameters_maystro/test-data/test_json_workflow2.json +++ b/tools/parameters_maystro/test-data/test_json_workflow2.json @@ -12,5 +12,6 @@ "table": "sample", "fragment_column": "fragment", "sequence_column": "sequence", - "annotation_column": "annotation" + "annotation_column": "annotation", + "methylation_protection": "true" } \ No newline at end of file From 914af3d9670b09174f8b8f1efed51312d13f8680 Mon Sep 17 00:00:00 2001 From: ramiz khaled Date: Fri, 5 Sep 2025 11:16:57 +0200 Subject: [PATCH 7/7] add tool: creat_assembly_picklists --- .../create_assembly_picklists.xml | 237 +++++++++++++++--- 1 file changed, 198 insertions(+), 39 deletions(-) diff --git a/tools/create_assembly_picklists/create_assembly_picklists.xml b/tools/create_assembly_picklists/create_assembly_picklists.xml index 6f8f250b..8ada9531 100644 --- a/tools/create_assembly_picklists/create_assembly_picklists.xml +++ b/tools/create_assembly_picklists/create_assembly_picklists.xml @@ -38,36 +38,62 @@ --parts_files '$renamed_paths' --picklist '$picklist' --source_plate 'source_plate.xlsx' - --backbone_name '$adv.backbone_name' - --part_backbone_ratio '$adv.part_backbone_ratio' - --quantity_unit '$quantity_unit' - --part_quantity '$part_quantity' - --buffer_volume '$buffer_volume' - --total_volume '$total_volume' - --dispenser '$dispenser' + --backbone_name '$setting.adv.backbone_name' + --part_backbone_ratio '$setting.adv.part_backbone_ratio' + --quantity_unit '$setting.quantity_unit' + --part_quantity '$setting.part_quantity' + --buffer_volume '$setting.buffer_volume' + --total_volume '$setting.total_volume' + --dispenser '$setting.dispenser' --result_zip 'picklist.zip' && cp 'picklist.zip' '$output_zip' ]]> - + + + + + + + + + + + + + + + + + + +
+ + +
+ + + + + + + + + + + + + + +
+ + +
+ + + - - - - - - - - - - - - -
- - -
@@ -173,11 +199,122 @@ - - - - - + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + + @@ -186,20 +323,42 @@ - `_ - -**Advance parameter**: ---------------------- -* **Backbone Name(s)**: It can be one backbone or more than one (one name by line) -* **Backbone Molar Ratio**: between 0.0 and 1.0 -This section is to multiplie the backbone concentration with the part:backbone molar ratio. This tricks the calculator into making a picklist with the desired ratio. For example, a part:backbone = 2:1 will multiply the backbone concentration by 2, therefore half as much of it will be added to the well. -**If Part quantity unit is ng**: Backbone Molar Ratio calculation is not performed in this case. - ]]> +`Read more... `_ + +**Advanced parameters:** +------------------------ + +- **Backbone Name(s):** It can be one backbone or more than one (one name per line). +- **Backbone Molar Ratio:** Between 0.0 and 1.0. This multiplies the backbone concentration with the part:backbone molar ratio. + For example, a part:backbone = 2:1 will multiply the backbone concentration by 2, so half as much of it will be added. + **Note:** If the part quantity unit is ng, this calculation is not performed. + +**Mode:** +--------- + +This option allows you to choose how the tool runs: + +- **Standard**: Runs the tool as a standalone application. +- **DEMO**: Runs the tool with demo data. + +Demo data: + +- **GenBank File(s):** `Download GenBank files `_ + + **Note:** Make GenBank files as a collection list. + `How to make collection `_ + +- **Assembly Plan (CSV or Excel):** `Download Assembly Plan `_ + +- **Source Plate (Excel):** `Download Source Plate `_ +]]> + + @unpublished{create_assembly_picklists