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SamT123SamT123
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Add genbank reference sequences
Fix final line warning rename M -> MP rename M -> MP Rename NS2 -> NS Fix tests
1 parent 929951b commit 663db55

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‎DESCRIPTION‎

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fs,
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purrr,
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readr,
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reticulate,
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stats,
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stringr
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Suggests:

‎NAMESPACE‎

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@@ -13,6 +13,8 @@ export(h1_epitope_positions)
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export(h3_epitope_positions)
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export(mafft_align)
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export(make_cmaple_tree)
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export(read_genbank)
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export(references)
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export(root_tree_using_outsequence)
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export(translate)
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export(write_fast_fasta)

‎R/reference_sequences.R‎

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#' Reference GenBank files
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#'
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#' A nested list of file paths to reference GenBank files bundled with the
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#' package. Access files like `references$H3N2$HA`.
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#'
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#' @export
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references <- NULL
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.onLoad <- function(libname, pkgname) {
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ref_dir <- system.file("extdata", "references", package = pkgname)
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subtypes <- list.dirs(ref_dir, recursive = FALSE, full.names = TRUE)
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refs <- lapply(subtypes, function(subtype_dir) {
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files <- list.files(subtype_dir, pattern = "\\.gb$", full.names = TRUE)
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setNames(as.list(files), tools::file_path_sans_ext(basename(files)))
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})
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names(refs) <- basename(subtypes)
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assign("references", refs, envir = parent.env(environment()))
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}
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#' Read a GenBank file
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#'
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#' Parses a GenBank file using BioPython's SeqIO, returning a structured list
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#' with sequence, annotations, and features (including CDS).
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#'
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#' Requires a Python installation with BioPython. BioPython will be installed
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#' automatically on first use if not already available.
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#'
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#' @param path Path to a GenBank (.gb) file.
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#' @return A list with elements: `id`, `name`, `description`, `sequence`,
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#' `annotations`, and `features`.
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#' @export
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read_genbank <- function(path) {
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reticulate::py_require("biopython")
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SeqIO <- reticulate::import("Bio.SeqIO", as = "SeqIO")
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record <- SeqIO$read(path, "genbank")
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list(
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id = record$id,
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name = record$name,
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description = record$description,
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sequence = record$seq$`__str__`(),
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annotations = as.list(record$annotations),
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features = purrr::map(
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record$features,
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function(f) {
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list(
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type = f$type,
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start = as.integer(f$location$start),
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end = as.integer(f$location$end),
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strand = as.integer(f$location$strand),
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qualifiers = as.list(f$qualifiers)
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)
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}
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)
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)
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}
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# Kept for backwards compatibility
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#' 550 aa HA sequence for Alaska/232/2015 (useful for aligning)
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#' @export
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alaska_232_2015_aas = "QKIPGNDNSTATLCLGHHAVPNGTIVKTITNDRIEVTNATELVQNSSIGEICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDLFVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACIRRSSSSFFSRLNWLTHLNYTYPALNVTMPNKEQFDKLYIWGVHHPGTDKDQIFLYAQSSGRITVSTKRSQQAVIPNIGSRPRIRDIPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKIRSGKSSIMRSDAPIGKCKSECITPNGSIPNDKPFQNVNRITYGACPRYVKHSTLKLATGMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGRGQAADLKSTQAAIDQINGKLNRLIGKTNEKFHQIEKEFSEVEGRVQDLEKYVEDTKIDLWSYNAELLVALENQHTIDLTDSEMNKLFEKTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNETYDHNVYRDEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVALLGFIMWACQKGNIRCNICI"
@@ -14,4 +76,4 @@ california_04_2009_h1_aas =
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#' nt HA sequence for Alaska/232/2015 (useful for aligning)
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#' @export
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california_04_2009_h1_nts =
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"GACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACACCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTATCTATCAGAATGCAGATACATATGTTTTTGTGGGGTCATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAAACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTGAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATATCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGCTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATT"
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"GACACATTATGTATAGGTTATCATGCGAACAATTCAACAGACACTGTAGACACAGTACTAGAAAAGAATGTAACAGTAACACACTCTGTTAACCTTCTAGAAGACAAGCATAACGGGAAACTATGCAAACTAAGAGGGGTAGCCCCATTGCATTTGGGTAAATGTAACATTGCTGGCTGGATCCTGGGAAATCCAGAGTGTGAATCACTCTCCACAGCAAGCTCATGGTCCTACATTGTGGAAACACCTAGTTCAGACAATGGAACGTGTTACCCAGGAGATTTCATCGATTATGAGGAGCTAAGAGAGCAATTGAGCTCAGTGTCATCATTTGAAAGGTTTGAGATATTCCCCAAGACAAGTTCATGGCCCAATCATGACTCGAACAAAGGTGTAACGGCAGCATGTCCTCATGCTGGAGCAAAAAGCTTCTACAAAAATTTAATATGGCTAGTTAAAAAAGGAAATTCATACCCAAAGCTCAGCAAATCCTACATTAATGATAAAGGGAAAGAAGTCCTCGTGCTATGGGGCATTCACCATCCATCTACTAGTGCTGACCAACAAAGTATCTATCAGAATGCAGATACATATGTTTTTGTGGGGTCATCAAGATACAGCAAGAAGTTCAAGCCGGAAATAGCAATAAGACCCAAAGTGAGGGATCAAGAAGGGAGAATGAACTATTACTGGACACTAGTAGAGCCGGGAGACAAAATAACATTCGAAGCAACTGGAAATCTAGTGGTACCGAGATATGCATTCGCAATGGAAAGAAATGCTGGATCTGGTATTATCATTTCAGATACACCAGTCCACGATTGCAATACAACTTGTCAAACACCCAAGGGTGCTATAAACACCAGCCTCCCATTTCAGAATATACATCCGATCACAATTGGAAAATGTCCAAAATATGTGAAAAGCACAAAATTGAGACTGGCCACAGGATTGAGGAATATCCCGTCTATTCAATCTAGAGGCCTATTTGGGGCCATTGCCGGTTTCATTGAAGGGGGGTGGACAGGGATGGTAGATGGATGGTACGGTTATCACCATCAAAATGAGCAGGGGTCAGGATATGCAGCCGACCTGAAGAGCACACAGAATGCCATTGACGAGATTACTAACAAAGTAAATTCTGTTATTGAAAAGATGAATACACAGTTCACAGCAGTAGGTAAAGAGTTCAACCACCTGGAAAAAAGAATAGAGAATTTAAATAAAAAAGTTGATGATGGTTTCCTGGACATTTGGACTTACAATGCCGAACTGTTGGTTCTATTGGAAAATGAAAGAACTTTGGACTACCACGATTCAAATGTGAAGAACTTATATGAAAAGGTAAGAAGCCAGCTAAAAAACAATGCCAAGGAAATTGGAAACGGCTGCTTTGAATTTTACCACAAATGCGATAACACGTGCATGGAAAGTGTCAAAAATGGGACTTATGACTACCCAAAATACTCAGAGGAAGCAAAATTAAACAGAGAAGAAATAGATGGGGTAAAGCTGGAATCAACAAGGATTTACCAGATTTTGGCGATCTATTCAACTGTCGCCAGTTCATTGGTACTGGTAGTCTCCCTGGGGGCAATCAGTTTCTGGATGTGCTCTAATGGGTCTCTACAGTGTAGAATATGTATT"

‎inst/extdata/references/H3N2/HA.gb‎

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LOCUS CY002064 1762 bp ss-RNA linear VRL 01-AUG-2005
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DEFINITION Influenza A virus (A/New York/392/2004(H3N2)) segment 4, complete
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sequence.
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ACCESSION CY002064
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VERSION CY002064.1
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KEYWORDS .
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SOURCE Influenza A virus (A/New York/392/2004(H3N2))
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ORGANISM Influenza A virus (A/New York/392/2004(H3N2))
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Viruses; Riboviria; Orthornavirae; Negarnaviricota;
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Polyploviricotina; Insthoviricetes; Articulavirales;
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Orthomyxoviridae; Alphainfluenzavirus; Alphainfluenzavirus
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influenzae.
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REFERENCE 1 (bases 1 to 1762)
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AUTHORS Ghedin,E., Miller,N., Zaborsky,J., Feldblyum,T., Subbu,V.,
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Shumway,M., Sitz,J., Kosack,D., Koo,H., Salzberg,S.L.,
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Griesemer,S., St. George,K., Bennett,R., Taylor,J., Bao,Y.,
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Bolotov,P., Dernovoy,D., Lipman,D.J. and Tatusova,T.
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TITLE The NIAID Influenza Genome Sequencing Project
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JOURNAL Unpublished
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REFERENCE 2 (bases 1 to 1762)
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CONSRTM The NIAID Influenza Genome Sequencing Consortium
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TITLE Direct Submission
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JOURNAL Submitted (01-AUG-2005) on behalf of TIGR/Wadsworth-NYSDOH/NCBI,
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National Center for Biotechnology Information, NIH, Bethesda, MD
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20894, USA
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FEATURES Location/Qualifiers
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source 1..1762
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/organism="Influenza A virus (A/New York/392/2004(H3N2))"
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/mol_type="genomic RNA"
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/strain="A/New York/392/2004"
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/serotype="H3N2"
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/isolation_source="gender:M; age:16y"
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/host="Homo sapiens"
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/db_xref="taxon:335341"
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/segment="4"
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/lab_host="RhMK 1 passage(s)"
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/geo_loc_name="USA: Tompkins County, NY"
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/collection_date="21-Dec-2004"
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gene 30..1730
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/gene="HA"
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CDS 30..1730
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/gene="HA"
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/function="receptor binding and fusion protein"
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/codon_start=1
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/product="hemagglutinin"
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/protein_id="AAZ38616.1"
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/translation="MKTIIALSYILCLVFAQKLPGNDNSTATLCLGHHAVPNGTIVKT
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ITNDQIEVTNATELVQSSSTGGICDSPHQILDGENCTLIDALLGDPQCDGFQNKKWDL
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FVERSKAYSNCYPYDVPDYASLRSLVASSGTLEFNNESFNWTGVTQNGTSSACKRRSN
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NSFFSRLNWLTHLKFKYPALNVTMPNNEKFDKLYIWGVHHPGTDNDQISLYAQASGRI
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TVSTKRSQQTVIPSIGSRPRIRDVPSRISIYWTIVKPGDILLINSTGNLIAPRGYFKI
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RSGKSSIMRSDAPIGKCNSECITPNGSIPNDKPFQNVNRITYGACPRYVKQNTLKLAT
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GMRNVPEKQTRGIFGAIAGFIENGWEGMVDGWYGFRHQNSEGTGQAADLKSTQAAINQ
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INGKLNRLIGKTNEKFHQIEKEFSEVEGRIQDLEKYVEDTKIDLWSYNAELLVALENQ
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HTIDLTDSEMNKLFERTKKQLRENAEDMGNGCFKIYHKCDNACIGSIRNGTYDHDVYR
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DEALNNRFQIKGVELKSGYKDWILWISFAISCFLLCVALLGFIMWACQKGNIRCNICI
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"
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sig_peptide 30..77
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/gene="HA"
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mat_peptide 78..1064
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/gene="HA"
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/product="HA1"
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mat_peptide 1065..1727
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/gene="HA"
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/product="HA2"
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ORIGIN
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1 agcaaaagca ggggataatt ctattaacca tgaagactat cattgctttg agctacattc
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61 tatgtctggt tttcgctcaa aaacttcccg gaaatgacaa cagcacggca acgctgtgcc
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121 ttgggcacca tgcagtacca aacggaacga tagtgaaaac aatcacgaat gaccaaattg
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181 aagtcactaa tgctactgaa ctggttcaga gttcctcaac aggtggaata tgcgacagtc
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241 ctcatcagat ccttgatgga gaaaactgca cactaataga tgctctattg ggagaccctc
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301 agtgtgatgg cttccaaaat aagaaatggg acctttttgt tgaacgcagc aaagcctaca
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361 gcaactgtta cccttatgat gtgccggatt atgcctccct taggtcacta gttgcctcat
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421 ccggcacact ggagtttaac aatgaaagct tcaattggac tggagtcact caaaatggaa
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481 caagctctgc ttgcaaaagg agatctaata acagtttctt tagtagattg aattggttga
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541 cccacttaaa attcaaatac ccagcattga acgtgactat gccaaacaat gaaaaatttg
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601 acaaactgta catttggggg gttcaccacc cgggtacgga caatgaccaa atcagcctat
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661 atgctcaagc atcaggaaga atcacagtct ctaccaaaag aagccaacaa accgtaatcc
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721 cgagtatcgg atctagaccc aggataaggg atgtccccag cagaataagc atctattgga
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781 caatagtaaa accgggagac atacttttga ttaacagcac agggaatcta attgctcctc
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841 ggggttactt caaaatacga agtgggaaaa gctcaataat gagatcagat gcacccattg
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901 gcaaatgcaa ttctgaatgc atcactccaa atggaagcat tcccaatgac aaaccatttc
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961 aaaatgtaaa caggatcaca tatggggcct gtcccagata tgttaagcaa aacactctga
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1021 aattggcaac agggatgcga aatgtaccag agaaacaaac tagaggcata tttggcgcaa
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1081 tcgcgggttt catagaaaat ggttgggagg gaatggtaga cggttggtac ggtttcaggc
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1141 atcaaaattc tgagggaaca ggacaagcag cagatctcaa aagcactcaa gcagcaatca
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1201 accaaatcaa tgggaagctg aataggttga tcgggaaaac aaacgagaaa ttccatcaga
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1261 ttgaaaaaga attctcagaa gtagaaggga gaattcagga cctcgagaaa tatgttgagg
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1321 acactaaaat agatctctgg tcatacaacg cggagcttct tgtggccctg gagaaccaac
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1381 atacaattga tctaactgac tcagaaatga acaaactgtt tgaaagaaca aagaagcaac
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1441 tgagggaaaa tgctgaggat atgggcaatg gttgtttcaa aatataccac aaatgtgaca
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1501 atgcctgcat agggtcaatc agaaatggaa cttatgacca tgatgtatac agagatgaag
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1561 cattaaacaa ccggttccag atcaaaggtg ttgagttgaa gtcaggatac aaagattgga
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1621 tcctatggat ttcctttgcc atatcatgtt ttttgctttg tgttgctttg ttggggttca
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1681 tcatgtgggc ctgccaaaaa ggcaacatta ggtgcaacat ttgcatttga gtgcattaat
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1741 taaaaacacc cttgtttcta ct
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//

‎inst/extdata/references/H3N2/MP.gb‎

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LOCUS CY002065 1027 bp ss-RNA linear VRL 01-AUG-2005
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DEFINITION Influenza A virus (A/New York/392/2004(H3N2)) segment 7, complete
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sequence.
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ACCESSION CY002065
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VERSION CY002065.1
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KEYWORDS .
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SOURCE Influenza A virus (A/New York/392/2004(H3N2))
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ORGANISM Influenza A virus (A/New York/392/2004(H3N2))
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Viruses; Riboviria; Orthornavirae; Negarnaviricota;
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Polyploviricotina; Insthoviricetes; Articulavirales;
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Orthomyxoviridae; Alphainfluenzavirus; Alphainfluenzavirus
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influenzae.
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REFERENCE 1 (bases 1 to 1027)
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AUTHORS Ghedin,E., Miller,N., Zaborsky,J., Feldblyum,T., Subbu,V.,
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Shumway,M., Sitz,J., Kosack,D., Koo,H., Salzberg,S.L.,
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Griesemer,S., St. George,K., Bennett,R., Taylor,J., Bao,Y.,
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Bolotov,P., Dernovoy,D., Lipman,D.J. and Tatusova,T.
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TITLE The NIAID Influenza Genome Sequencing Project
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JOURNAL Unpublished
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REFERENCE 2 (bases 1 to 1027)
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CONSRTM The NIAID Influenza Genome Sequencing Consortium
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TITLE Direct Submission
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JOURNAL Submitted (01-AUG-2005) on behalf of TIGR/Wadsworth-NYSDOH/NCBI,
24+
National Center for Biotechnology Information, NIH, Bethesda, MD
25+
20894, USA
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FEATURES Location/Qualifiers
27+
source 1..1027
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/organism="Influenza A virus (A/New York/392/2004(H3N2))"
29+
/mol_type="genomic RNA"
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/strain="A/New York/392/2004"
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/serotype="H3N2"
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/isolation_source="gender:M; age:16y"
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/host="Homo sapiens"
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/db_xref="taxon:335341"
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/segment="7"
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/lab_host="RhMK 1 passage(s)"
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/geo_loc_name="USA: Tompkins County, NY"
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/collection_date="21-Dec-2004"
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gene 26..1007
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/gene="M2"
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CDS join(26..51,740..1007)
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/gene="M2"
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/codon_start=1
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/product="matrix protein 2"
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/protein_id="AAZ38618.1"
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/translation="MSLLTEVETPIRNEWGCRCNDSSDPLVVAASIIGILHLILWILD
47+
RLFFKCVYRLFKHGLKRGPSTEGVPESMREEYRKEQQNAVDADDSHFVSIELE"
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gene 26..784
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/gene="M1"
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CDS 26..784
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/gene="M1"
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/codon_start=1
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/product="matrix protein 1"
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/protein_id="AAZ38617.1"
55+
/translation="MSLLTEVETYVLSIVPSGPLKAEIAQRLEDVFAGKNTDLEALME
56+
WLKTRPILSPLTKGILGFVFTLTVPSERGLQRRRFVQNALNGNGDPNNMDKAVKLYRK
57+
LKREITFHGAKEIALSYSAGALASCMGLIYNRMGAVTTEVAFGLVCATCEQIADSQHR
58+
SHRQMVATTNPLIKHENRMVLASTTAKAMEQMAGSSEQAAEAMEIASQARQMVQAMRA
59+
VGTHPSSSTGLRDDLLENLQTYQKRMGVQMQRFK"
60+
ORIGIN
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1 agcaaaagca ggtagatatt gaaagatgag ccttctaacc gaggtcgaaa cgtatgttct
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61 ctctatcgtt ccatcaggcc ccctcaaagc cgagatcgcg cagagacttg aagatgtctt
63+
121 tgctgggaaa aacacagatc ttgaggctct catggaatgg ctaaagacaa gaccaattct
64+
181 gtcacctctg actaagggga ttttggggtt tgtgttcacg ctcaccgtgc ccagtgagcg
65+
241 aggactgcag cgtagacgct ttgtccaaaa tgccctcaat gggaatggag atccaaataa
66+
301 catggacaaa gcagttaaac tgtataggaa acttaagagg gagataacgt tccatggggc
67+
361 caaagaaata gctctcagtt attctgctgg tgcacttgcc agttgcatgg gcctcatata
68+
421 caataggatg ggggctgtaa ccactgaagt ggcatttggc ctggtatgtg caacatgtga
69+
481 acagattgct gactcccagc acaggtctca taggcaaatg gtggcaacaa ccaatccatt
70+
541 aataaaacat gagaacagaa tggttttggc cagcactaca gctaaggcta tggagcaaat
71+
601 ggctggatca agtgagcagg cagcggaggc catggaaatt gctagtcagg ccaggcaaat
72+
661 ggtgcaggca atgagagccg ttgggactca tcctagctcc agtactggtc taagagatga
73+
721 tcttcttgaa aatttgcaga cctatcagaa acgaatgggg gtgcagatgc aacgattcaa
74+
781 gtgacccgct tgttgttgcc gcgagtatca ttgggatctt gcacttgata ttgtggattc
75+
841 ttgatcgtct ttttttcaaa tgcgtctatc gactcttcaa acacggcctt aaaagaggcc
76+
901 cttctacgga aggagtacct gagtctatga gggaagaata tcgaaaggaa cagcagaatg
77+
961 ctgtggatgc tgacgacagt cattttgtca gcatagagtt ggagtaaaaa actaccttgt
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1021 ttctact
79+
//

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