--- a/collapseBed2.py	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,36 +0,0 @@
-'''
-collapse intervals
-'''
-
-def collapseInterval_strand(filename,c_strand,c_score):
-    # keeping max column c
-    uniqintv = {}
-    data = {}
-    f = open(filename)
-    header = f.readline()
-    if 'chr' in header:
-        flds = header.strip().split('\t')
-        key = '\t'.join([flds[0],flds[1],flds[2],flds[c_strand]])
-        uniqintv[key] = float(flds[c_score])
-        data[key] = flds
-    for line in f:
-        flds = line.strip().split('\t')
-        key = '\t'.join([flds[0],flds[1],flds[2],flds[c_strand]])
-        if not uniqintv.has_key(key):
-            uniqintv[key] = float(flds[c_score])
-            data[key] = flds
-        elif uniqintv[key] < float(flds[c_score]):
-            uniqintv[key] = float(flds[c_score])
-            data[key] = flds
-            
-    f.close()        
-    for key in uniqintv.keys():
-        print '\t'.join(data[key])
-        
-import sys
-
-if sys.argv[2] == '0':#ignore strand
-    sys.argv[2] = 1
-if sys.argv[3] == '0':# ignore score
-    sys.argv[3] = 2
-collapseInterval_strand(sys.argv[1],int(sys.argv[2])-1,int(sys.argv[3])-1)