erange version 4.0a dev release

[erange.git] / geneNeighbors.py

diff --git a/geneNeighbors.py b/geneNeighbors.py
index 8ec363c77fdbacaa39534d8debe1a65abb1962bb..221ffe215e2ca1c9b21560334329e7b0fbe1ba66 100755 (executable)
--- a/geneNeighbors.py
+++ b/geneNeighbors.py
@@ -9,12 +9,13 @@ try:
 except:
     pass
 
-import sys, optparse
-from commoncode import getMergedRegions, getLocusByChromDict
+import sys
+import optparse
+from commoncode import getMergedRegions, getLocusByChromDict, getConfigParser, getConfigIntOption, getConfigBoolOption, getConfigOption
 from cistematic.genomes import Genome
-from cistematic.core.geneinfo import geneinfoDB
+from commoncode import getGeneInfoDict
 
-print "%prog: version 2.4"
+print "geneNeighbors: version 2.5" % sys.argv[0]
 
 
 def main(argv=None):
@@ -23,16 +24,7 @@ def main(argv=None):
 
     usage = "usage: python %prog genome outfilename [--regions acceptfile] [--downstream bp] [--upstream bp] [--mindist bp] [--minlocus bp] [--maxlocus bp] [--samesense]"
 
-    parser = optparse.OptionParser(usage=usage)
-    parser.add_option("--regions", dest="acceptFile")
-    parser.add_option("--downstream", type="int", dest="downMax")
-    parser.add_option("--upstream", type="int", dest="upMax")
-    parser.add_option("--mindist", type="int", dest="minDist")
-    parser.add_option("--minlocus", type="int", dest="minLocus")
-    parser.add_option("--maxlocus", type="int", dest="maxLocus")
-    parser.add_option("--samesense", action="store_true", dest="checkSense")
-    parser.set_defaults(acceptfile="", checkSense=False, downMax=10000000,
-                        upMax=10000000, minDist=0, minLocus=-1, maxLocus=10000000)
+    parser = getParser(usage)
     (options, args) = parser.parse_args(argv[1:])
 
     if len(args) < 2:
@@ -49,6 +41,32 @@ def main(argv=None):
     print "\n%d genes matched" % index
 
 
+def getParser(usage):
+    parser = optparse.OptionParser(usage=usage)
+    parser.add_option("--regions", dest="acceptFile")
+    parser.add_option("--downstream", type="int", dest="downMax")
+    parser.add_option("--upstream", type="int", dest="upMax")
+    parser.add_option("--mindist", type="int", dest="minDist")
+    parser.add_option("--minlocus", type="int", dest="minLocus")
+    parser.add_option("--maxlocus", type="int", dest="maxLocus")
+    parser.add_option("--samesense", action="store_true", dest="checkSense")
+
+    configParser = getConfigParser()
+    section = "geneNeighbors"
+    acceptfile = getConfigOption(configParser, section, "acceptfile", "")
+    checkSense = getConfigBoolOption(configParser, section, "checkSense", False)
+    downMax = getConfigIntOption(configParser, section, "downMax", 10000000)
+    upMax = getConfigIntOption(configParser, section, "upMax", 10000000)
+    minDist = getConfigIntOption(configParser, section, "minDist", 0)
+    minLocus = getConfigIntOption(configParser, section, "minLocus", -1)
+    maxLocus = getConfigIntOption(configParser, section, "maxLocus", 10000000)
+
+    parser.set_defaults(acceptfile=acceptfile, checkSense=checkSense, downMax=downMax,
+                        upMax=upMax, minDist=minDist, minLocus=minLocus, maxLocus=maxLocus)
+
+    return parser
+
+
 def geneNeighbors(genome, outfilename, acceptfile="", checkSense=False,
                   downMax=10000000, upMax=10000000, minDist=0, minLocus=-1,
                   maxLocus=10000000):
@@ -58,17 +76,15 @@ def geneNeighbors(genome, outfilename, acceptfile="", checkSense=False,
         acceptDict = getMergedRegions(acceptfile, maxDist=0, keepLabel=True, verbose=True)
 
     hg = Genome(genome)
-    idb = geneinfoDB(cache=True)
-
-    geneinfoDict = idb.getallGeneInfo(genome)
+    geneinfoDict = getGeneInfoDict(genome, cache=True)
     locusByChromDict = getLocusByChromDict(hg, additionalRegionsDict=acceptDict, keepSense=True)
 
     gidList = hg.allGIDs()
     gidList.sort()
     for chrom in acceptDict:
-        for (label, start, stop, length) in acceptDict[chrom]:
-            if label not in gidList:
-                gidList.append(label)
+        for region in acceptDict[chrom]:
+            if region.label not in gidList:
+                gidList.append(region.label)
 
     index = 0
     outfile = open(outfilename,"w")