Mercurial > repos > yufei-luo > s_mart
diff SMART/Java/Python/CountLoci.py @ 31:0ab839023fe4
Uploaded
author | m-zytnicki |
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date | Tue, 30 Apr 2013 14:33:21 -0400 |
parents | 94ab73e8a190 |
children |
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--- 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)