| Previous changeset 56:97aa2e42bfdf (2014-02-05) Next changeset 58:5f5c9b74c2dd (2014-02-07) |
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SMART/Java/Python/RemoveExons.py SMART/galaxy/.removeIntrons.xml.swp |
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| diff -r 97aa2e42bfdf -r 36eaa579fdb6 SMART/Java/Python/RemoveExons.py --- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/Java/Python/RemoveExons.py Fri Feb 07 08:29:48 2014 -0500 |
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| @@ -0,0 +1,75 @@ +#! /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. +# +from optparse import OptionParser +from commons.core.parsing.ParserChooser import ParserChooser +from commons.core.writer.TranscriptWriter import TranscriptWriter +from SMART.Java.Python.structure.Transcript import Transcript +from SMART.Java.Python.misc.Progress import Progress + +class RemoveExons(object): + + def __init__(self, verbosity): + self.verbosity = verbosity + self.selection = False + + def setInputFile(self, fileName, format): + chooser = ParserChooser(self.verbosity) + chooser.findFormat(format) + self.parser = chooser.getParser(fileName) + + def setOutputFile(self, fileName): + self.writer = TranscriptWriter(fileName, "gff3", self.verbosity) + + def run(self): + progress = Progress(self.parser.getNbTranscripts(), "Reading input file", self.verbosity) + for transcript in self.parser.getIterator(): + transcript.removeExons() + self.writer.addTranscript(transcript) + progress.inc() + self.writer.write() + self.writer.close() + progress.done() + +if __name__ == "__main__": + + description = "Remove Exons v1.0.1: Excluse the exons of a set of transcripts. [Category: Data Modification]" + + parser = OptionParser(description = description) + parser.add_option("-i", "--input", dest="inputFileName", action="store", type="string", help="input file [compulsory] [format: file in transcript format given by -f]") + parser.add_option("-f", "--format", dest="format", action="store", type="string", help="format of file [compulsory] [format: transcript file format]") + parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]") + parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]") + (options, args) = parser.parse_args() + + re = RemoveExons(options.verbosity) + re.setInputFile(options.inputFileName, options.format) + re.setOutputFile(options.outputFileName) + re.run() |
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| diff -r 97aa2e42bfdf -r 36eaa579fdb6 SMART/galaxy/.removeIntrons.xml.swp |
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| Binary file SMART/galaxy/.removeIntrons.xml.swp has changed |