Mercurial > repos > yufei-luo > s_mart

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

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Uploaded
author m-zytnicki
date Tue, 30 Apr 2013 14:33:21 -0400
parents 94ab73e8a190
children
comparison
equal deleted inserted replaced
30:5677346472b5 31:0ab839023fe4
35 from commons.core.writer.Gff3Writer import Gff3Writer 35 from commons.core.writer.Gff3Writer import Gff3Writer
36 from commons.core.writer.TranscriptWriter import TranscriptWriter 36 from commons.core.writer.TranscriptWriter import TranscriptWriter
37 from SMART.Java.Python.misc.Progress import Progress 37 from SMART.Java.Python.misc.Progress import Progress
38 from SMART.Java.Python.misc.RPlotter import RPlotter 38 from SMART.Java.Python.misc.RPlotter import RPlotter
39 from SMART.Java.Python.cleanGff import CleanGff 39 from SMART.Java.Python.cleanGff import CleanGff
40 from SMART.Java.Python.CompareOverlappingSmallRef import CompareOverlappingSmallRef 40 from SMART.Java.Python.CompareOverlapping import CompareOverlapping
41 from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator 41 from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
42 from SMART.Java.Python.GetUpDownStream import GetUpDownStream 42 from SMART.Java.Python.GetUpDownStream import GetUpDownStream
43 43
44 REFERENCE = 0 44 REFERENCE = 0
45 QUERY = 1 45 QUERY = 1
83 def _getReferenceFiles(self): 83 def _getReferenceFiles(self):
84 self.referenceFiles = {"CDS": "%scds.gff3" % (self.outputBase), \ 84 self.referenceFiles = {"CDS": "%scds.gff3" % (self.outputBase), \
85 "five_prime_UTR": "%sfive.gff3" % (self.outputBase), \ 85 "five_prime_UTR": "%sfive.gff3" % (self.outputBase), \
86 "three_prime_UTR": "%sthree.gff3" % (self.outputBase), \ 86 "three_prime_UTR": "%sthree.gff3" % (self.outputBase), \
87 "mRNA": "%smrna.gff3" % (self.outputBase), \ 87 "mRNA": "%smrna.gff3" % (self.outputBase), \
88 "ncRNA": "%sncRNA.gff3" % (self.outputBase), \ 88 "ncRNA": "%sncRNA.gff3" % (self.outputBase), \
89 "transposable_element_gene": "%sTE.gff3" % (self.outputBase), \ 89 "transposable_element_gene": "%sTE.gff3" % (self.outputBase), \
90 "vic": "%svicinity.gff3" % (self.outputBase)} 90 "vic": "%svicinity.gff3" % (self.outputBase)}
91 self.tmpFileNames.extend(self.referenceFiles.values()) 91 self.tmpFileNames.extend(self.referenceFiles.values())
92 for tag, fileName in self.referenceFiles.iteritems(): 92 for tag, fileName in self.referenceFiles.iteritems():
93 if tag == "ncRNA": 93 if tag == "ncRNA":
96 continue 96 continue
97 else: 97 else:
98 self._writeTmpRef([tag], fileName) 98 self._writeTmpRef([tag], fileName)
99 99
100 def _compare(self, queryFileName, queryFormat, referenceFileName, referenceFormat, outputFileName, exclusion = False): 100 def _compare(self, queryFileName, queryFormat, referenceFileName, referenceFormat, outputFileName, exclusion = False):
101 co = CompareOverlappingSmallRef(self.verbosity-1) 101 co = CompareOverlapping(self.verbosity-1)
102 co.setQueryFile(queryFileName, queryFormat) 102 co.setInput(queryFileName, queryFormat, QUERY)
103 co.setReferenceFile(referenceFileName, referenceFormat) 103 co.setInput(referenceFileName, referenceFormat, REFERENCE)
104 co.setOutputFile(outputFileName) 104 co.setOutput(outputFileName)
105 if exclusion: 105 if exclusion:
106 co.setInvert(True) 106 co.getInvert(True)
107 co.run() 107 co.run()
108 return co.nbWritten 108 return co._nbOverlappingQueries
109 109
110 def _copy(self, inputFile, tag): 110 def _copy(self, inputFile, tag):
111 parser = GffParser(inputFile, self.verbosity-1) 111 parser = GffParser(inputFile, self.verbosity-1)
112 for transcript in parser.getIterator(): 112 for transcript in parser.getIterator():
113 transcript.setTagValue("locus", tag) 113 transcript.setTagValue("locus", tag)