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comparison convertEnsembl.py @ 14:76e1b1b21cce default tip

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author xuebing
date Tue, 13 Mar 2012 19:05:10 -0400
parents 292186c14b08
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13:292186c14b08 14:76e1b1b21cce
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