Mercurial > repos > yufei-luo > s_mart
diff SMART/Java/Python/SelectByTag.py @ 6:769e306b7933
Change the repository level.
author | yufei-luo |
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date | Fri, 18 Jan 2013 04:54:14 -0500 |
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--- /dev/null Thu Jan 01 00:00:00 1970 +0000 +++ b/SMART/Java/Python/SelectByTag.py Fri Jan 18 04:54:14 2013 -0500 @@ -0,0 +1,148 @@ +#! /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. +# +"""Select the transcript such that a tag value is not less than a given threshold""" +import os +import sys +from optparse import OptionParser +from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer +from commons.core.writer import MySqlTranscriptWriter +from commons.core.writer.Gff3Writer import Gff3Writer +from SMART.Java.Python.misc.Progress import Progress +from SMART.Java.Python.misc.RPlotter import RPlotter + +class SelectByTag(object): + + def __init__(self, verbosity = 1): + self.input = None + self.format = None + self.tag = None + self.value = None + self.min = None + self.max = None + self.default = None + self.output = None + self.mysql = None + self.verbosity = verbosity + + self.parser = None + self.writer = None + self.mysqlWriter = None + self.nbElements = None + self.nbWritten = 0 + + + def setParser(self): + self.parser = TranscriptContainer(self.input, self.format, self.verbosity) + self.nbElements = self.parser.getNbTranscripts() + + + def setWriter(self): + self.writer = Gff3Writer(self.output, self.verbosity) + if self.mysql: + self.mysqlWriter = MySqlTranscriptWriter(self.output, self.verbosity) + + + def isAccepted(self, transcript): + value = transcript.getTagValue(self.tag) + if value == None: + if self.default != None: + value = self.default + else: + raise Exception("Error! Transcript %s no tag called '%s'" % (transcript, self.tag)) + if self.value != None: + if self.value == str(value): + return True + return self.value.isdigit() and value == float(self.value) + value = float(value) + return (self.min == None or self.min <= value) and (self.max == None or self.max >= value) + + + def readInputFile(self): + progress = Progress(self.parser.getNbTranscripts(), "Writing transcripts", self.verbosity) + for transcript in self.parser.getIterator(): + if self.isAccepted(transcript): + self.writer.addTranscript(transcript) + if self.mysql: + self.mysqlWriter.addTranscript(transcript) + self.nbWritten += 1 + progress.inc() + progress.done() + + + def writeFile(self): + self.writer.write() + if self.mysql: + self.mysqlWriter.write() + + + def run(self): + self.setParser() + self.setWriter() + self.readInputFile() + self.writeFile() + if self.verbosity > 0: + print "%d input" % (self.nbElements) + if self.nbElements != 0: + print "%d output (%.2f%%)" % (self.nbWritten, float(self.nbWritten) / self.nbElements * 100) + + + +if __name__ == "__main__": + + # parse command line + description = "Select by Tag v1.0.2: Keep the genomic coordinates such that a the value of a given tag is between two limits. [Category: Data Selection]" + + 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 the input [compulsory] [format: transcript file format]") + parser.add_option("-g", "--tag", dest="tag", action="store", default=None, type="string", help="the tag [compulsory] [format: string]") + parser.add_option("-a", "--value", dest="value", action="store", default=None, type="string", help="the value to be found [format: string]") + parser.add_option("-m", "--min", dest="min", action="store", default=None, type="float", help="the minimum threshold [format: float]") + parser.add_option("-M", "--max", dest="max", action="store", default=None, type="float", help="the maximum threshold [format: float]") + parser.add_option("-d", "--default", dest="default", action="store", default=None, type="float", help="value if tag is not present [format: float]") + parser.add_option("-o", "--output", dest="outputFileName", action="store", type="string", help="output file [format: output file in GFF3 format]") + parser.add_option("-y", "--mysql", dest="mysql", action="store_true", default=False, help="write output into MySQL tables [format: boolean] [default: False]") + parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]") + (options, args) = parser.parse_args() + + selectByTag = SelectByTag(options.verbosity) + selectByTag.input = options.inputFileName + selectByTag.format = options.format + selectByTag.tag = options.tag + selectByTag.value = options.value + selectByTag.min = options.min + selectByTag.max = options.max + selectByTag.default = options.default + selectByTag.output = options.outputFileName + selectByTag.mysql = options.mysql + selectByTag.run() + +