fix_macaque_gaps

IMGT’s gapped FASTA sequences for rhesus macaque IGHV, IGLV and IGKV contain inserted codons relative to the sequences for most other species. These additional codons in macaque sequences cause problems for downstream tools such as Change-o that expect features such as CDRs and conserved residues to be present at specific co-ordinates. This utility restores the ‘standard’ alignment by removing the inserted codons. A small number of sequences in the IMGT sets use these codons: the tool lists those sequences and removes them from the set. Personally I have not observed these sequences in rhesus repertoires, but this is something that you may wish to check before using the set produced by the tool.

Remove unwanted inserted codons in IMGT alignment of rhesus macaque IG sequences

usage: fix_macaque_gaps [-h] infile outfile chain

Positional Arguments

infile

gapped file from IMGT

outfile

gapped file confirming to the customary alignment (without inserted codons)

chain

IGH, IGK or IGL