Mercurial > repos > davidvanzessen > vidjil_with_browser

comparison germline/split-from-imgt.py @ 0:fe4001bdf8d4 draft

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author davidvanzessen
date Tue, 09 Dec 2014 03:55:01 -0500
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-1:000000000000 0:fe4001bdf8d4
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3 import sys
4
5 # Parse lines in IMGT/GENE-DB such as:
6 # >M12949|TRGV1*01|Homo sapiens|ORF|...
7
8 open_files = {}
9 current_file = None
10
11 for l in sys.stdin:
12
13 if ">" in l:
14 current_file = None
15 if "Homo sapiens" in l and ("V-REGION" in l or "D-REGION" in l or "J-REGION" in l):
16 system = l.split('|')[1][:4]
17 if system.startswith('IG') or system.startswith('TR'):
18
19 if system in open_files:
20 current_file = open_files[system]
21 else:
22 name = '%s.fa' % system
23 print " ==>", name
24 current_file = open(name, 'w')
25 open_files[system] = current_file
26
27
28 if current_file:
29 current_file.write(l)
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