UniprotIdRetrieval

Downloads protein sequences from Uniprot, in the desired output format, based on the given ids (either passed as arguments or identified in a file)

Dependencies

• Python 2.7
• Module dependencies (run pip install -r requirements.txt to install):
  • requests

How to run

Runs through the command line, like so:

UniprotIdRetrieval.py [-h] (-f <file> | -i <id ...>) [-fo {fasta, gff, tab, txt, rdf, xml}]

• -h, --help shows the help text
• -f, --file takes a file path to search for ids
• -i, --ids takes 1 or more ids
• -fo, --format defines the output format of downloaded files (fasta, gff, tab, txt, rdf or xml), defaults to 'fasta'