diff fimo2bed.py @ 14:76e1b1b21cce default tip

Deleted selected files

--- a/fimo2bed.py	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,46 +0,0 @@
-'''
-#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')