Python-programming-for-life-science-researchers

This is a repository containing scripts for the course project. The repository includes scripts to download and analyze sequences.

Information

DownloadMitoGenBanks:

• ExtractGenBankIDs.py: Extracts GenBank IDs from a list of mitochondrial genomes
• MitoGenomeList.txt: File used for testing ExtractGenBankIDs.py
• MitoLocusIDs.txt: File generated by ExtractGenBankIDs.py and used as input for DownloadGenBank
• DownloadGenBank.py: Script for downloading GenBank files from NCBI

DownloadGenomeGenBanks:

• getGenomeGenBanks: Script for downloading genbank files for entire genome using FTP
• GenomeList.txt: List of genomes used as input for getGenomeGenBanks.py
• MitoGenomeList.txt: List of mitochondrial genomes used as input for getGenomeGenBanks.py

Analysis:

• AnalyzeSequence.py: Script used to analyze the codon and amino acid usage of the coding sequence of a genome
• calculateGCcontent.py: Script used to analyze the GC content of the coding sequence of a genome
• NC_001224.1.gb: GenBank file used for testing the scripts for analysis

Miscellaneous:

• CheckGenBank.py: Script that checks if the genome sequence is present in the GenBank file
• ConvertGenBank.py: Script that converts a GenBank file to FASTA (.fna) format
• NC_001224.1.gb: GenBank file used for testing scripts

How to run the code

./pythonfile.py

Requirements

• Python 2.7
• bioython version 1.69
• matplotlib version 2.0.2