Commit 3105a36c authored by Mikaël Salson's avatar Mikaël Salson

split-from-imgt: clean/comment

parent fc4d106b
Pipeline #33012 passed with stages
in 57 minutes and 29 seconds
......@@ -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)
......
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