extract_refs

This utility will extract sections from an IMGT gapped reference file, or download the file and extract. The latest file can also be downloaded here.

Extract reference files for nominated species from a gapped IMGT reference file

usage: extract_refs [-h] [-r REF] [-L LOCUS] [-F] species_name

Positional Arguments

species_name

species name for IMGT file in quotes, e.g. “Homo sapiens”, “Macaca mulatta”

Named Arguments

-r, --ref

gapped imgt reference file. If not specified, the current file will be downloaded from http://www.imgt.org/download/GENE-DB/IMGTGENEDB-ReferenceSequences.fasta-nt-WithGaps-F+ORF+inframeP

-L, --locus

locus identifier, e.g. “IGH” (default), “IGK”, “TRB”, “TRG”

Default: “IGH”

-F, --functional_only

Default: False