Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/cleaning/GtfCleaner.py @ 25:7809e72960fe
Deleted selected files
author | m-zytnicki |
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date | Mon, 29 Apr 2013 03:29:14 -0400 |
parents | 769e306b7933 |
children | 97aa2e42bfdf |
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#! /usr/bin/env python # # Copyright INRA-URGI 2009-2010 # # This software is governed by the CeCILL license under French law and # abiding by the rules of distribution of free software. You can use, # modify and/ or redistribute the software under the terms of the CeCILL # license as circulated by CEA, CNRS and INRIA at the following URL # "http://www.cecill.info". # # As a counterpart to the access to the source code and rights to copy, # modify and redistribute granted by the license, users are provided only # with a limited warranty and the software's author, the holder of the # economic rights, and the successive licensors have only limited # liability. # # In this respect, the user's attention is drawn to the risks associated # with loading, using, modifying and/or developing or reproducing the # software by the user in light of its specific status of free software, # that may mean that it is complicated to manipulate, and that also # therefore means that it is reserved for developers and experienced # professionals having in-depth computer knowledge. Users are therefore # encouraged to load and test the software's suitability as regards their # requirements in conditions enabling the security of their systems and/or # data to be ensured and, more generally, to use and operate it in the # same conditions as regards security. # # The fact that you are presently reading this means that you have had # knowledge of the CeCILL license and that you accept its terms. # """ Clean a GTF file """ import shlex from SMART.Java.Python.cleaning.TranscriptListCleaner import TranscriptListCleaner from SMART.Java.Python.misc.Progress import Progress from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress count = {} class ParsedLine(object): def __init__(self, line, cpt): self.line = line self.cpt = cpt self.parse() def parse(self): self.line = self.line.strip() self.splittedLine = self.line.split(None, 8) if len(self.splittedLine) < 9: raise Exception("Line '%s' has less than 9 fields. Exiting..." % (self.line)) self.type = self.splittedLine[2] self.parseOptions() def parseOptions(self): self.parsedOptions = {} key = None value = "" for option in shlex.split(self.splittedLine[8]): option = option.strip() if option == "": continue if key == None: key = option else: endValue = False if option[-1] == ";": endValue = True option.rstrip(";") value = "%s \"%s\"" % (value, option) if endValue: self.parsedOptions[key] = value if key == "transcript_id": self.transcriptId = value key = None value = "" def export(self): return "%s\n" % (self.line) class GtfCleaner(TranscriptListCleaner): def __init__(self, verbosity = 1): super(GtfCleaner, self).__init__(verbosity) self.acceptedTypes = ["exon"] self.parents = {} def getFileFormats(): return ["gtf"] getFileFormats = staticmethod(getFileFormats) def setAcceptedTypes(self, types): self.acceptedTypes = types def parse(self): progress = UnlimitedProgress(100000, "Reading input file", self.verbosity) for cpt, line in enumerate(self.inputHandle): if not line or line[0] == "#": continue parsedLine = ParsedLine(line, cpt) if self.acceptedTypes == None or parsedLine.type in self.acceptedTypes: transcriptId = parsedLine.transcriptId if transcriptId not in self.parents: self.parents[parsedLine.transcriptId] = [parsedLine] else: self.parents[parsedLine.transcriptId].append(parsedLine) progress.inc() progress.done() def write(self): progress = Progress(len(self.parents.keys()), "Writing output file", self.verbosity) for parent in sorted(self.parents.keys()): for line in self.parents[parent]: self.outputHandle.write(line.export()) progress.inc() progress.done() def _clean(self): self.parse() self.write()