From 3105a36ccf519737146b0b389ff1d949ae6a3867 Mon Sep 17 00:00:00 2001 From: Mikael Salson Date: Thu, 12 Jul 2018 20:30:14 +0200 Subject: [PATCH] split-from-imgt: clean/comment --- germline/split-from-imgt.py | 5 ++++- 1 file changed, 4 insertions(+), 1 deletion(-) diff --git a/germline/split-from-imgt.py b/germline/split-from-imgt.py index be0d14021..2dd2abc0a 100644 --- a/germline/split-from-imgt.py +++ b/germline/split-from-imgt.py @@ -135,12 +135,15 @@ def retrieve_genes(f, genes, tag, additional_length, gene_list): if gene_id: try: (target, start, end) = ncbi.get_gene_positions(gene_id) - print(coord, gene_id, target, start, end) except KeyError: print('! No positions for %s (%s: %s)' % (gene_id, gene, str(coord))) allele_additional_length = additional_length gene_id = None + # gene: is the name of the sequence where the VDJ gene was identified according to IMGT. The gene is just a part of the sequence + # gene_id: is the NCBI ID of the VDJ gene + # target: is the NCBI ID of the chromosome + # extract from gene gene_data = ncbi.get_gene_sequence(gene, coord['imgt_data'] + tag, coord['from'], coord['to'], allele_additional_length) -- GitLab