From fc39377e6cc56d9d17478bd9bee8bbf330a2cd0a Mon Sep 17 00:00:00 2001
From: depristo <depristo@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Thu, 4 Nov 2010 20:34:43 +0000
Subject: [PATCH] Simple pre-processing script for soapsnp files

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4627 348d0f76-0448-11de-a6fe-93d51630548a
---
 python/fixSoapSnp.py | 23 +++++++++++++++++++++++
 1 file changed, 23 insertions(+)
 create mode 100644 python/fixSoapSnp.py

diff --git a/python/fixSoapSnp.py b/python/fixSoapSnp.py
new file mode 100644
index 000000000..dbd0b545c
--- /dev/null
+++ b/python/fixSoapSnp.py
@@ -0,0 +1,23 @@
+import os.path
+import sys
+from optparse import OptionParser
+
+
+def main():
+    global OPTIONS
+    usage = "usage: %prog [options] cmap input.soapsnp"
+    parser = OptionParser(usage=usage)
+    
+    (OPTIONS, args) = parser.parse_args()
+    if len(args) != 2:
+        parser.error("Requires exactly 2 arguments")
+
+    cmap = dict([reversed(line.split()) for line in open(args[0])])
+    #print cmap
+    for line in open(args[1]):
+        parts = line.split()
+        mapped = cmap[parts[0]]
+        print "\t".join([mapped] + parts[1:])
+
+if __name__ == "__main__":
+    main()
\ No newline at end of file