Modified to work with MT containing VCFs.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3910 348d0f76-0448-11de-a6fe-93d51630548a

python/vcf_b36_to_hg18.py

@@ -1,5 +1,5 @@
 from farm_commands2 import *
-import os.path
+import os
 import sys
 from optparse import OptionParser
 from datetime import date
@@ -24,15 +24,20 @@ def main():
 
     b36vcf, hg18vcf = args
 
-    out = open(hg18vcf, 'w')
+    temp = open("tmp", 'w')
+    mitotemp = open("mtmp",'w')
     for line in open(b36vcf):
         length = len(line)
         if length > 2 and line[0] != '#':
             if line[0:2] == 'MT':
-                sys.exit('Cannot convert MT containing VCFs, sorry')
+                spline = line.split("\t")
+                spline[0] = "chrM"
+                mitotemp.write("\t".join(spline))
             line = 'chr' + line
-        out.write(line)
+        temp.write(line)
     out.close()
+    mitotemp.close()
+    os.system("cat mtmp tmp > "+hg18vcf+" ; rm mtmp ; rm tmp")
 
 if __name__ == "__main__":
     main()