vquest 0.0.10

Automate IMGT V-QUEST usage on imgt.org

Automate IMGT V-QUEST usage on imgt.org

IMGT's V-QUEST is only available via a web interface. This Python package automates V-QUEST usage by submitting request data like the web form does. Currently only the "Download AIRR formatted results" option is supported.

Example command-line usage, with rhesus sequences in seqs.fasta:

pip install . # or skip this and use "python -m vquest" below
vquest --species rhesus-monkey --receptorOrLocusType IG --fileSequences seqs.fasta

The output is saved to Parameters.txt and vquest_airr.tsv (the files V-QUEST provides in a zip archive) in the working directory by default.

Or with --align to automatically extract the alignment as FASTA:

vquest --align --species rhesus-monkey --receptorOrLocusType IG --fileSequences seqs.fasta

Here the aligned FASTA text is printed directly to standard output.

Example Python usage:

>>> from vquest.vq import *
>>> config = layer_configs(DEFAULTS, {"species": "rhesus-monkey", "receptorOrLocusType": "IG", "fileSequences": "seqs.fasta"})
>>> result = vquest(config)
>>> result.keys()
dict_keys(['Parameters.txt', 'vquest_airr.tsv'])

Here the output is a dictionary of filenames to contents.

The only required options are species, receptorOrLocusType, and either fileSequences or sequences (to provide sequences directly as text). Options can be given via command-line arguments or one or more YAML configuration files. See data/defaults.yml and ./vquest.py --help for details.

The web form will only accept 50 sequences at a time, so the sequences given here are grouped into chunks of 50, submitted, and (by default) the results automatically combined. A delay (default 1 second) is used between submissions to avoid being impolite to the server.

• V-QUEST: http://www.imgt.org/IMGT_vquest/analysis
• V-QUEST docs: http://www.imgt.org/IMGT_vquest/user_guide#intro
• A different approach, using Selenium to automate V-QUEST usage with a browser: https://github.com/AndrewZoldy/IMGT_VQUEST_BOT