--- a/collapseBed.py	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,58 +0,0 @@
-'''
-collapse intervals
-'''
-
-def collapseInterval_strand(filename):
-    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[5]])
-        uniqintv[key] = 1
-        data[key] = flds
-    for line in f:
-        flds = line.strip().split('\t')
-        key = '\t'.join([flds[0],flds[1],flds[2],flds[5]])
-        if uniqintv.has_key(key):
-            uniqintv[key] = uniqintv[key] + 1
-        else:
-            uniqintv[key] = 1
-            data[key] = flds
-    f.close()        
-    for key in uniqintv.keys():
-        print '\t'.join(data[key]+[str(uniqintv[key])])
-        #flds = key.split('\t')
-        #print '\t'.join([flds[0],flds[1],flds[2],'.',str(uniqintv[key]),flds[3]])
-
-def collapseInterval(filename):
-    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]])
-        uniqintv[key] = 1
-        data[key] = flds
-    for line in f:
-        flds = line.strip().split('\t')
-        key = '\t'.join([flds[0],flds[1],flds[2]])
-        if uniqintv.has_key(key):
-            uniqintv[key] = uniqintv[key] + 1
-        else:
-            uniqintv[key] = 1
-            data[key] = flds
-    f.close()        
-    for key in uniqintv.keys():
-        print '\t'.join(data[key]+[str(uniqintv[key])])
-        #flds = key.split('\t')
-        #print '\t'.join([flds[0],flds[1],flds[2],'.',str(uniqintv[key])])       
-
-import sys
-
-if sys.argv[2] == 'strand':
-    collapseInterval_strand(sys.argv[1])
-else:
-    collapseInterval(sys.argv[1])