diff SMART/Java/Python/CountLoci.py @ 31:0ab839023fe4

Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
line wrap: on
line diff
--- a/SMART/Java/Python/CountLoci.py	Mon Apr 29 03:45:52 2013 -0400
+++ b/SMART/Java/Python/CountLoci.py	Tue Apr 30 14:33:21 2013 -0400
@@ -37,7 +37,7 @@
 from SMART.Java.Python.misc.Progress import Progress
 from SMART.Java.Python.misc.RPlotter import RPlotter
 from SMART.Java.Python.cleanGff import CleanGff
-from SMART.Java.Python.CompareOverlappingSmallRef import CompareOverlappingSmallRef
+from SMART.Java.Python.CompareOverlapping import CompareOverlapping
 from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
 from SMART.Java.Python.GetUpDownStream import GetUpDownStream
 
@@ -85,7 +85,7 @@
                                "five_prime_UTR":            "%sfive.gff3"     % (self.outputBase), \
                                "three_prime_UTR":           "%sthree.gff3"    % (self.outputBase), \
                                "mRNA":                      "%smrna.gff3"     % (self.outputBase), \
-                               "ncRNA":                     "%sncRNA.gff3"    % (self.outputBase), \
+                               "ncRNA":                     "%sncRNA.gff3"     % (self.outputBase), \
                                "transposable_element_gene": "%sTE.gff3"       % (self.outputBase), \
                                "vic":                       "%svicinity.gff3" % (self.outputBase)}
         self.tmpFileNames.extend(self.referenceFiles.values())
@@ -98,14 +98,14 @@
                 self._writeTmpRef([tag], fileName)
 
     def _compare(self, queryFileName, queryFormat, referenceFileName, referenceFormat, outputFileName, exclusion = False):
-        co = CompareOverlappingSmallRef(self.verbosity-1)
-        co.setQueryFile(queryFileName, queryFormat)
-        co.setReferenceFile(referenceFileName, referenceFormat)
-        co.setOutputFile(outputFileName)
+        co = CompareOverlapping(self.verbosity-1)
+        co.setInput(queryFileName, queryFormat, QUERY)
+        co.setInput(referenceFileName, referenceFormat, REFERENCE)
+        co.setOutput(outputFileName)
         if exclusion:
-            co.setInvert(True)
+            co.getInvert(True)
         co.run()
-        return co.nbWritten
+        return co._nbOverlappingQueries
 
     def _copy(self, inputFile, tag):
         parser = GffParser(inputFile, self.verbosity-1)