diff tools/mytools/convertEnsembl.py @ 0:9071e359b9a3

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/tools/mytools/convertEnsembl.py	Fri Mar 09 19:37:19 2012 -0500
@@ -0,0 +1,26 @@
+'''
+convert ensembl bed to ucsc
+add chr to chromosome
+1 = +
+-1 = -
+'''
+
+import sys
+f = open(sys.argv[1])
+out = open(sys.argv[2],'w')
+skip = int(sys.argv[3])
+
+for i in range(skip):
+    f.readline()
+
+for line in f:
+    flds = line.strip().split('\t')
+    flds[0] = 'chr'+flds[0]
+    if flds[5] == '1':
+        flds[5] = '+'
+    else:
+        flds[5] = '-'
+    out.write('\t'.join(flds)+'\n')
+f.close()
+out.close()
+