Mercurial > repos > xuebing > sharplab_seq_motif
view mytools/fimo2bed.py @ 5:84e2c77a6abd
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author | xuebing |
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date | Fri, 16 Mar 2012 14:01:16 -0400 |
parents | 39217fa39ff2 |
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''' #pattern name sequence name start stop score p-value q-value matched sequence constitutive-donor mm9_chr1_39533592_39535592_- 1815 1823 12.032 4.26e-06 0.397 CAGGTAAGT constitutive-donor mm9_chr1_59313750_59315750_+ 1889 1897 12.032 4.26e-06 0.397 CAGGTAAGT #pattern name sequence name start stop score p-value q-value matched sequence constitutive-donor mm9_chr1_172019075_172021075_- 1947 1955 12.032 4.26e-06 0.843 CAGGTAAGT constitutive-donor mm9_chr1_15300532_15302532_+ 156 164 12.032 4.26e-06 0.843 CAGGTAAGT ''' import sys def fimo2bed(filename,rc): ''' parse fimo output to make a bed file rc: the sequence have been reverse complemented ''' f = open(filename) header = f.readline() for line in f: pattern,posi,begin,stop,score,pv,qv,seq = line.strip().split('\t') flds = posi.split('_') start = flds[-3] end = flds[-2] strand = flds[-1] chrom = '_'.join(flds[1:-3]) #'chrX_random' if not rc: if strand == '+': start1 = str(int(start) + int(begin)-1) end1 = str(int(start) + int(stop)) print '\t'.join([chrom,start1,end1,seq,score,strand]) else: start1 = str(int(end) - int(stop)) end1 = str(int(end) - int(begin)+1) print '\t'.join([chrom,start1,end1,seq,score,strand]) else: if strand == '-': start1 = str(int(start) + int(begin)-1) end1 = str(int(start) + int(stop)) print '\t'.join([chrom,start1,end1,seq,score,'+']) else: start1 = str(int(end) - int(stop)) end1 = str(int(end) - int(begin)+1) print '\t'.join([chrom,start1,end1,seq,score,'-']) fimo2bed(sys.argv[1],sys.argv[2]=='rc')