simple tool that takes two dbSNP files and subsets the seconds to only include rsID SNPs present in the first. Used to make b129 against b37 by subsetting b131/b37 vs. b129/b36

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3352 348d0f76-0448-11de-a6fe-93d51630548a

python/subsetDbSNPWithrsIDs.py

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+import sys
+from optparse import OptionParser
+
+def getRsIDSet(dbSNPIds, idIndex):
+    s = set()
+    for line in open(dbSNPIds):
+        #print line
+        rsID = line.split()[idIndex]
+        s.add(rsID)
+
+    return frozenset(s)
+
+
+def main():
+    global OPTIONS
+    usage = "usage: %prog [options] dbSNP.in.rsids dbSNP.to.match dbSNP.out"
+    parser = OptionParser(usage=usage)
+    parser.add_option("-v", "--verbose", dest="verbose",
+                        action='store_true', default=False,
+                        help="")
+                        
+    (OPTIONS, args) = parser.parse_args()
+    if len(args) != 3:
+        parser.error("incorrect number of arguments")
+
+    dbSNPIds = args[0]
+    dbSNPMatch = args[1]
+    dbSNPOut = args[2]
+    idIndex = 4
+
+    rsSet = getRsIDSet(dbSNPIds, idIndex)
+    print 'rsID set has %d elements' % len(rsSet)
+    
+    # 
+    count = 0
+    matched = 0 
+    out = open(dbSNPOut, 'w')
+    for line in open(dbSNPMatch):
+        count += 1
+        rsID = line.split()[idIndex]
+        if rsID in rsSet:
+            #sys.stdout.write(line)
+            matched += 1
+            out.write(line)
+    print 'Processed %d lines, matching %d elements, excluding %d' % ( count, matched, count - matched )
+    out.close()
+            
+if __name__ == "__main__":
+    main()