parse_imgt_annotations

parse_imgt_annotations downloads an IMGT annotation file or or uses a file already downloaded. It parses the file to provide a list of annotated features. Optionally it will also store the file downloaded, and create a FASTA file containing the annotated assembly. Please refer to Annotating the human IGH locus for example usage.

Given a set of IMGT annotations, build a CSV file containing gene names and co-ordinates

usage: parse_imgt_annotations [-h] [--save_download SAVE_DOWNLOAD] [--save_sequence SAVE_SEQUENCE] [--save_imgt_annots SAVE_IMGT_ANNOTS] imgt_url outfile locus

Positional Arguments

imgt_url

URL of IMGT annotation, e.g. http://www.imgt.org/ligmdb/view?format=IMGT&id=IMGT000064, or name of text file containing its contents

outfile

Output file (CSV)

locus

one of IGH, IGK, IGL, TRA, TRB, TRD, TRG

Named Arguments

--save_download

Save contents of annotation to specified file

--save_sequence

Save sequence to specified file

--save_imgt_annots

Save IMGT annotations to specified file