Mercurial > repos > yufei-luo > s_mart

comparison SMART/Java/Python/cleaning/GtfCleaner.py @ 56:97aa2e42bfdf

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Uploaded
author m-zytnicki
date Wed, 05 Feb 2014 11:51:11 -0500
parents 769e306b7933
children
comparison
equal deleted inserted replaced
55:2ac71607aa60 56:97aa2e42bfdf
94 self.acceptedTypes = types 94 self.acceptedTypes = types
95 95
96 def parse(self): 96 def parse(self):
97 progress = UnlimitedProgress(100000, "Reading input file", self.verbosity) 97 progress = UnlimitedProgress(100000, "Reading input file", self.verbosity)
98 for cpt, line in enumerate(self.inputHandle): 98 for cpt, line in enumerate(self.inputHandle):
99 if not line or line[0] == "#": continue 99 if not line or (not line.strip()) or line[0] == "#": continue
100 parsedLine = ParsedLine(line, cpt) 100 parsedLine = ParsedLine(line, cpt)
101 if self.acceptedTypes == None or parsedLine.type in self.acceptedTypes: 101 if self.acceptedTypes == None or parsedLine.type in self.acceptedTypes:
102 transcriptId = parsedLine.transcriptId 102 transcriptId = parsedLine.transcriptId
103 if transcriptId not in self.parents: 103 if transcriptId not in self.parents:
104 self.parents[parsedLine.transcriptId] = [parsedLine] 104 self.parents[parsedLine.transcriptId] = [parsedLine]