Mercurial > repos > xuebing > sharplabtool

comparison mytools/convertEnsembl.py @ 9:87eb5c5ddfe9

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Uploaded
author xuebing
date Fri, 09 Mar 2012 20:01:43 -0500
parents f0dc65e7f6c0
children
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8:361ec1c0479d 9:87eb5c5ddfe9
1 '''
2 convert ensembl bed to ucsc
3 add chr to chromosome
4 1 = +
5 -1 = -
6 '''
7
8 import sys
9 f = open(sys.argv[1])
10 out = open(sys.argv[2],'w')
11 skip = int(sys.argv[3])
12
13 for i in range(skip):
14 f.readline()
15
16 for line in f:
17 flds = line.strip().split('\t')
18 flds[0] = 'chr'+flds[0]
19 if flds[5] == '1':
20 flds[5] = '+'
21 else:
22 flds[5] = '-'
23 out.write('\t'.join(flds)+'\n')
24 f.close()
25 out.close()
26