Commit ef1a2464 authored by Mathieu Giraud's avatar Mathieu Giraud
Browse files

split-from-imgt.py: get_gene_sequence works with NCBI 'simplified FASTA headers'

See https://www.ncbi.nlm.nih.gov/news/09-17-2014-simple-FASTA-headers-genomes-FTP/
Fixes #2173.
parent 539708b0
......@@ -85,7 +85,7 @@ def get_gene_sequence(gene, other_gene_name, start, end):
Return the gene sequences between positions start and end (included).
'''
fasta_string = urllib.urlopen(NCBI_API % (gene, start, end)).read()
return re.sub('(>g.\|)', r'\1'+other_gene_name+'|', fasta_string)
return re.sub('(>\S*) ', r'\1|'+other_gene_name+'|', fasta_string)
def store_data_if_updownstream(fasta_header, path, data, genes):
for gene in gene_matches(fasta_header, genes):
......
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