useful chain files

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5660 348d0f76-0448-11de-a6fe-93d51630548a

chainFiles/makeChains.py

@@ -0,0 +1,50 @@
+#!/bin/tcsh
+import os.path
+import sys
+from optparse import OptionParser
+from itertools import *
+
+def main():
+    global OPTIONS
+    usage = "usage: %prog [options] mode hg19Tohg18.chain"
+    parser = OptionParser(usage=usage)
+    
+#     parser.add_option("-D", "--delete_while_archiving", dest="reallyDeleteInArchiveMode",
+#                         action='store_true', default=False,
+#                         help="if provided, we'll actually delete records when running in archive mode")
+         
+    (OPTIONS, args) = parser.parse_args()
+    if len(args) != 1:
+        parser.error("Requires exact 1 chain to analyze")
+
+    hg192hg18 = args[0]
+    
+    writeChain(hg192hg18, "b37tohg18.chain", lambda x: hg2b(x, 2))
+    writeChain(hg192hg18, "b37tob36.chain", lambda x: hg2b(hg2b(x, 2), 7))
+    
+HG2BCONTIG = dict()
+for c in range(1, 23) + ["X", "Y"]:
+    HG2BCONTIG["chr" + str(c)] = str(c)
+HG2BCONTIG["chrM"] = "MT"
+    
+def hg2b(line, pos):
+    parts = line.split()
+    if len(parts) > pos and "chr" in parts[pos]:
+        if parts[pos] in HG2BCONTIG:
+            parts[pos] = HG2BCONTIG[parts[pos]]
+        else:
+            print 'Skipping ', parts[pos]
+    return "\t".join(parts)
+    
+def writeChain(inFile, outFile, transform):
+    out = open(outFile, "w")
+    for line in open(inFile):
+        newLine = transform(line)
+        #print 'newline', newLine
+        if newLine != None:
+            out.write(newLine)
+            out.write("\n")
+    out.close()
+
+if __name__ == "__main__":
+    main()