Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/clusterize.py @ 46:169d364ddd91

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Uploaded
author m-zytnicki
date Mon, 30 Sep 2013 03:19:26 -0400
parents 44d5973c188c
children 90f4b29d884f
comparison
equal deleted inserted replaced
45:e454402ba9d9 46:169d364ddd91
102 progress = UnlimitedProgress(10000, "Reading input file", self.verbosity) 102 progress = UnlimitedProgress(10000, "Reading input file", self.verbosity)
103 parser = self.parser 103 parser = self.parser
104 else: 104 else:
105 progress = Progress(self.nbElementsPerChromosome[chromosome], "Checking chromosome %s" % (chromosome), self.verbosity) 105 progress = Progress(self.nbElementsPerChromosome[chromosome], "Checking chromosome %s" % (chromosome), self.verbosity)
106 parser = NCListFileUnpickle(self.splittedFileNames[chromosome], self.verbosity) 106 parser = NCListFileUnpickle(self.splittedFileNames[chromosome], self.verbosity)
107 transcripts = [] 107 transcripts = []
108 self.nbElements = 0
109 for newTranscript in parser.getIterator(): 108 for newTranscript in parser.getIterator():
110 newTranscripts = [] 109 newTranscripts = []
111 if newTranscript.__class__.__name__ == "Mapping": 110 if newTranscript.__class__.__name__ == "Mapping":
112 newTranscript = newTranscript.getTranscript() 111 newTranscript = newTranscript.getTranscript()
113 for oldTranscript in transcripts: 112 for oldTranscript in transcripts:
117 self._write(oldTranscript) 116 self._write(oldTranscript)
118 else: 117 else:
119 newTranscripts.append(oldTranscript) 118 newTranscripts.append(oldTranscript)
120 newTranscripts.append(newTranscript) 119 newTranscripts.append(newTranscript)
121 transcripts = newTranscripts 120 transcripts = newTranscripts
122 self.nbElements += 1
123 progress.inc() 121 progress.inc()
124 for transcript in transcripts: 122 for transcript in transcripts:
125 self._write(transcript) 123 self._write(transcript)
126 progress.done() 124 progress.done()
127 125