annotate SMART/Java/Python/SelectByTag.py @ 6:769e306b7933

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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.
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# 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()