Commit 2771e711 authored by Mathieu Giraud's avatar Mathieu Giraud

get-germline, split-from-imgt.py: retrieve also IMGTGENEDB-GeneList and use stored files

See #3009
parent 65a03851
#!/bin/sh
cd $(dirname $0)
wget -O - http://www.imgt.org/download/GENE-DB/IMGTGENEDB-ReferenceSequences.fasta-nt-WithGaps-F+ORF+inframeP | python split-from-imgt.py
wget http://www.imgt.org/download/GENE-DB/IMGTGENEDB-GeneList
wget http://www.imgt.org/download/GENE-DB/IMGTGENEDB-ReferenceSequences.fasta-nt-WithGaps-F+ORF+inframeP
python split-from-imgt.py IMGTGENEDB-ReferenceSequences.fasta-nt-WithGaps-F+ORF+inframeP IMGTGENEDB-GeneList
wget -O IMGT_RELEASE http://www.imgt.org/download/GENE-DB/RELEASE
......
......@@ -223,7 +223,10 @@ class OrderedDefaultListDict(OrderedDict):
downstream_data = defaultdict(lambda: OrderedDefaultListDict())
upstream_data = defaultdict(lambda: OrderedDefaultListDict())
for l in sys.stdin:
ReferenceSequences = sys.argv[1]
GeneList = sys.argv[2]
for l in open(ReferenceSequences):
# New sequence: compute 'current_files' and stores up/downstream_data[]
......
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