Mercurial > repos > davidvanzessen > vidjil_with_browser
view germline/split-from-imgt.py @ 6:7346cd210a43 draft
Uploaded
author | davidvanzessen |
---|---|
date | Thu, 12 Feb 2015 09:54:07 -0500 |
parents | fe4001bdf8d4 |
children |
line wrap: on
line source
import sys # Parse lines in IMGT/GENE-DB such as: # >M12949|TRGV1*01|Homo sapiens|ORF|... open_files = {} current_file = None for l in sys.stdin: if ">" in l: current_file = None if "Homo sapiens" in l and ("V-REGION" in l or "D-REGION" in l or "J-REGION" in l): system = l.split('|')[1][:4] if system.startswith('IG') or system.startswith('TR'): if system in open_files: current_file = open_files[system] else: name = '%s.fa' % system print " ==>", name current_file = open(name, 'w') open_files[system] = current_file if current_file: current_file.write(l)