Mercurial > repos > yufei-luo > s_mart
view SMART/Java/Python/CombineTags.py @ 56:97aa2e42bfdf
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author | m-zytnicki |
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date | Wed, 05 Feb 2014 11:51:11 -0500 |
parents | 769e306b7933 |
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#! /usr/bin/env python # # Copyright INRA-URGI 2009-2011 # # 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. # import os import random from optparse import OptionParser from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer from SMART.Java.Python.misc.Progress import Progress from commons.core.parsing.ParserChooser import ParserChooser from commons.core.writer.Gff3Writer import Gff3Writer OPERATIONS = ("plus", "minus", "times", "div") class CombineTags(object): def __init__(self, verbosity = 0): self.verbosity = verbosity def setInputFile(self, fileName, format): self.inputFileName = fileName parserChooser = ParserChooser(self.verbosity) parserChooser.findFormat(format, "transcript") self.parser = parserChooser.getParser(fileName) def setOutputFile(self, fileName): self.outputWriter = Gff3Writer(fileName, self.verbosity) def setTags(self, tag1, tag2, outputTag, defaultValue = None): self.tag1 = tag1 self.tag2 = tag2 self.outputTag = outputTag self.defaultValue = defaultValue def setOperation(self, operation): self.operation = operation if self.operation not in OPERATIONS: raise Exception("Do no handle operation %s, only: %s" % (self.operation, ", ".join(OPERATIONS))) def run(self): progress = Progress(self.parser.getNbTranscripts(), "Printing transcripts %s" % (self.inputFileName), self.verbosity) for transcript in self.parser.getIterator(): tag1 = transcript.getTagValue(self.tag1) tag2 = transcript.getTagValue(self.tag2) if tag1 == None or tag2 == None: if self.defaultValue == None: raise Exception("Transcript %s misses one of the tags %s and %s, and has no default value !" % (transcript, self.tag1, self.tag2)) newTag = self.defaultValue else: tag1, tag2 = float(tag1), float(tag2) if self.operation == "plus": newTag = tag1 + tag2 elif self.operation == "minus": newTag = tag1 - tag2 elif self.operation == "times": newTag = tag1 * tag2 elif self.operation == "div": newTag = tag1 / tag2 transcript.setTagValue(self.outputTag, newTag) self.outputWriter.addTranscript(transcript) progress.inc() progress.done() self.parser.close() self.outputWriter.close() if __name__ == "__main__": # parse command line description = "Change Tag Name v1.0.1: Change the name of tag of a list 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", "--inputFormat", dest="inputFormat", action="store", type="string", help="format of the input file [compulsory] [format: transcript file format]") parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [compulsory] [format: output file in GFF3 format]") parser.add_option("-t", "--tag1", dest="tag1", action="store", type="string", help="name of the first tag [compulsory] [format: string]") parser.add_option("-T", "--tag2", dest="tag2", action="store", type="string", help="name of the second tag [compulsory] [format: string]") parser.add_option("-d", "--default", dest="defaultValue", action="store", default=None, type="string", help="default value when one of the tag is absent [compulsory] [format: float]") parser.add_option("-n", "--new", dest="newTag", action="store", type="string", help="name of the new tag [compulsory] [format: string]") parser.add_option("-p", "--operation", dest="operation", action="store", type="string", help="operation combining the tags [compulsory] [format: choice (plus, minus, times, div)]") parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int] [default: 1]") (options, args) = parser.parse_args() combiner = CombineTags(options.verbosity) combiner.setInputFile(options.inputFileName, options.inputFormat) combiner.setOutputFile("%s.gff3" % (options.outputFileName)) combiner.setTags(options.tag1, options.tag2, options.newTag, options.defaultValue) combiner.setOperation(options.operation) combiner.run()