name_allele

Name an allele by comparing to a reference set. Construct a novel name containing SNPs if necessary. Use extract_refs to create suitable reference sets.

usage: name_allele [-h] [-g GENE_NAME] [-r] ref_set sequence

Positional Arguments

ref_set

reference set containing sequences from a single locus (e.g. IGH, TRB) (FASTA) (V genes should be IMGT-gapped)

sequence

input sequence

Named Arguments

-g, --gene

only consider reference sequences from the specified gene

-r, --rev_comp

reverse-complement sequence before processing

Default: False