Quick script that changes "chr#" to "#" and "chrM" to "MT" and moves mitochondria to the end of the vcf; in accordance with the 1KG reference.

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2727 348d0f76-0448-11de-a6fe-93d51630548a

python/generate1KGHapmapVCF.py

@@ -0,0 +1,29 @@
+#!/usr/bin/env python
+
+import os
+
+hapmap_dir = os.getcwd()+"/" ##CHANGE ME
+
+def convert(line):
+    line = line.replace("chr","",1)
+    if ( line.startswith("M") ):
+        line = line.replace("M","MT",1)
+    return line
+
+for file in os.listdir(hapmap_dir):
+    if ( file.endswith('vcf') ):
+        chrM_lines = list()
+        print("converting: "+file)
+        in_vcf = open(hapmap_dir+file)
+        out_vcf_filename = file.replace("hg18","b36")
+        out_vcf = open(out_vcf_filename,'w')
+        for line in in_vcf.readlines():
+            if ( line.startswith("#") ):
+                out_vcf.write(line)
+            else:
+                if ( line.startswith("chrM") ):
+                    chrM_lines.append(line)
+                else:
+                    out_vcf.write(convert(line))
+        for line in chrM_lines:
+            out_vcf.write(convert(line))