X-Git-Url: http://woldlab.caltech.edu/gitweb/?p=erange.git;a=blobdiff_plain;f=getSNPGeneInfo.py;h=0fbc6795121db515e27151902531f0962aa05715;hp=307413b866e804e831e2288a14a6c0984a55b5bf;hb=HEAD;hpb=5e4ae21098dba3d1edcf11e7279da0d84c3422e4

diff --git a/getSNPGeneInfo.py b/getSNPGeneInfo.py
index 307413b..0fbc679 100755
--- a/getSNPGeneInfo.py
+++ b/getSNPGeneInfo.py
@@ -16,9 +16,9 @@ import sys
 import optparse
 import string
 from cistematic.core import genesIntersecting, cacheGeneDB, uncacheGeneDB
-from cistematic.core.geneinfo import geneinfoDB
+from commoncode import getGeneInfoDict, getConfigParser, getConfigBoolOption, getConfigIntOption
 
-print "%prog: version 4.5"
+print "getSNPGeneInfo: version 4.6"
 
 def main(argv=None):
     if not argv:
@@ -26,11 +26,7 @@ def main(argv=None):
 
     usage = "usage: python %prog genome snpsfile rpkmfile dbsnp_geneinfo_outfile [--cache] [--withoutsense] [--flank bp]"
 
-    parser = optparse.OptionParser(usage=usage)
-    parser.add_option("--cache", action="store_true", dest="cachePages")
-    parser.add_option("--withoutsense", action="store_false", dest="withSense")
-    parser.add_option("--flank", type="int", dest="flankBP")
-    parser.set_defaults(doCache=False, withSense=True, flankBP=0)
+    parser = makeParser(usage)
     (options, args) = parser.parse_args(argv[1:])
 
     if len(args) < 4:
@@ -45,6 +41,23 @@ def main(argv=None):
     writeSNPGeneInfo(genome, infilename, rpkmfilename, outfilename, options.doCache, options.withSense, options.flankBP)
 
 
+def makeParser(usage=""):
+    parser = optparse.OptionParser(usage=usage)
+    parser.add_option("--cache", action="store_true", dest="cachePages")
+    parser.add_option("--withoutsense", action="store_false", dest="withSense")
+    parser.add_option("--flank", type="int", dest="flankBP")
+
+    configParser = getConfigParser()
+    section = "getSNPGeneInfo"
+    doCache = getConfigBoolOption(configParser, section, "doCache", False)
+    withSense = getConfigBoolOption(configParser, section, "withSense", True)
+    flankBP = getConfigIntOption(configParser, section, "flankBP", 0)
+
+    parser.set_defaults(doCache=doCache, withSense=withSense, flankBP=flankBP)
+
+    return parser
+
+
 def writeSNPGeneInfo(genome, infilename, rpkmfilename, outfilename, doCache=False, withSense=True, flankBP=0):
 
     outList = getSNPGeneInfo(genome, infilename, rpkmfilename, doCache, withSense, flankBP)
@@ -85,12 +98,9 @@ def getSNPGeneInfo(genome, infilename, rpkmfilename, doCache=False, withSense=Tr
 
     if doCache:
         cacheGeneDB(genome)
-        idb = geneinfoDB(cache=True)
         print "cached %s" % genome
-    else:
-        idb = geneinfoDB()
 
-    geneinfoDict = idb.getallGeneInfo(genome)
+    geneinfoDict = getGeneInfoDict(genome, cache=doCache)
     geneDict = {}
 
     if flankBP > 0:
@@ -106,7 +116,7 @@ def getSNPGeneInfo(genome, infilename, rpkmfilename, doCache=False, withSense=Tr
             symbol = "LOC%s" % geneID
 
         geneDescriptor = (symbol, geneID)
-        if geneDict.has_key(geneDescriptor):
+        if geneDescriptor in geneDict:
             geneDict[geneDescriptor]["position"].append(pos)
         else:
             geneDict[geneDescriptor] = {"position": [pos],
@@ -157,7 +167,7 @@ def getSNPGeneInfoList(geneDict, snpDict, rpkmDict, withSense):
                                "geneID": geneID}
 
             rpkm = "N\A"
-            if rpkmDict.has_key(geneID):
+            if geneID in rpkmDict:
                 rpkm = str(rpkmDict[geneID])
 
             snpGeneInfoDict["rpkm"] = rpkm