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comparison mytools/fimo2bed.py @ 7:f0dc65e7f6c0

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author xuebing
date Fri, 09 Mar 2012 19:59:07 -0500
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6:094f377db4e5 7:f0dc65e7f6c0
1 '''
2 #pattern name sequence name start stop score p-value q-value matched sequence
3 constitutive-donor mm9_chr1_39533592_39535592_- 1815 1823 12.032 4.26e-06 0.397 CAGGTAAGT
4 constitutive-donor mm9_chr1_59313750_59315750_+ 1889 1897 12.032 4.26e-06 0.397 CAGGTAAGT
5
6 #pattern name sequence name start stop score p-value q-value matched sequence
7 constitutive-donor mm9_chr1_172019075_172021075_- 1947 1955 12.032 4.26e-06 0.843 CAGGTAAGT
8 constitutive-donor mm9_chr1_15300532_15302532_+ 156 164 12.032 4.26e-06 0.843 CAGGTAAGT
9 '''
10
11 import sys
12
13 def fimo2bed(filename,rc):
14 '''
15 parse fimo output to make a bed file
16 rc: the sequence have been reverse complemented
17 '''
18 f = open(filename)
19 header = f.readline()
20 for line in f:
21 pattern,posi,begin,stop,score,pv,qv,seq = line.strip().split('\t')
22 flds = posi.split('_')
23 start = flds[-3]
24 end = flds[-2]
25 strand = flds[-1]
26 chrom = '_'.join(flds[1:-3]) #'chrX_random'
27 if not rc:
28 if strand == '+':
29 start1 = str(int(start) + int(begin)-1)
30 end1 = str(int(start) + int(stop))
31 print '\t'.join([chrom,start1,end1,seq,score,strand])
32 else:
33 start1 = str(int(end) - int(stop))
34 end1 = str(int(end) - int(begin)+1)
35 print '\t'.join([chrom,start1,end1,seq,score,strand])
36 else:
37 if strand == '-':
38 start1 = str(int(start) + int(begin)-1)
39 end1 = str(int(start) + int(stop))
40 print '\t'.join([chrom,start1,end1,seq,score,'+'])
41 else:
42 start1 = str(int(end) - int(stop))
43 end1 = str(int(end) - int(begin)+1)
44 print '\t'.join([chrom,start1,end1,seq,score,'-'])
45
46 fimo2bed(sys.argv[1],sys.argv[2]=='rc')