--- a/bedClean.py	Sat Mar 10 08:17:36 2012 -0500
+++ /dev/null	Thu Jan 01 00:00:00 1970 +0000
@@ -1,37 +0,0 @@
-import sys
-
-def readChrSize(filename):
-    f = open(filename)
-    chrSize = {}
-    for line in f:
-        chrom,size = line.strip().split()
-        chrSize[chrom]=int(size)
-    f.close()
-    return chrSize
-
-def cleanFile(filename,chrSize,outfile):
-    f = open(filename)
-    out = open(outfile,'w')
-    i = 0
-    for line in f:
-        i = i + 1
-        flds = line.strip().split('\t')
-        if len(flds) < 3:
-            print 'line',i,'incomplete line:\n',line
-        elif chrSize.has_key(flds[0]):
-            if int(flds[1]) > int(flds[2]):
-                tmp = flds[1]
-                flds[1] = flds[2]
-                flds[2] = tmp
-            if int( flds[1]) < 0 or int(flds[2]) <0:
-                print 'line',i,'negative coordinates:\n',line
-            elif int(flds[2]) > chrSize[flds[0]]:
-                print 'line',i,'end larger than chr size:\n',line
-            else:
-                out.write('\t'.join(flds)+'\n')
-        else:
-            print 'line',i,'chromosome',flds[0],'not found!\n',line
-    f.close()
-    out.close()
-
-cleanFile(sys.argv[1],readChrSize(sys.argv[2]),sys.argv[3])