view smart_toolShed/SMART/Java/Python/mappingToCoordinates.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

#! /usr/bin/env python
#
# Copyright INRA-URGI 2009-2010
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# abiding by the rules of distribution of free software. You can use,
# modify and/ or redistribute the software under the terms of the CeCILL
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# "http://www.cecill.info".
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"""Convert files with some mapping format to coordinates format"""

import os
from optparse import OptionParser
from commons.core.parsing.PslParser import PslParser
from commons.core.parsing.AxtParser import AxtParser
from commons.core.writer.Gff3Writer import Gff3Writer
from commons.core.writer.MySqlTranscriptWriter import MySqlTranscriptWriter
from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
from SMART.Java.Python.misc.Progress import Progress


class MappingToCoordinates(object):
    def __init__(self,verbosity=1, inputFileName=None, format = None, output=None,galaxy = False, title="S-MART"):
        self.verbosity = verbosity
        self.inputFileName = inputFileName
        self.format = format
        self.output = output
        self.galaxy = galaxy
        self.title = title
    
    def setAttributesFromCmdLine(self):
        description = "Mapping To Coordinates v1.0.1: Convert a set of mappings (given by a mapping tool) to a set of transcripts. [Category: Conversion]"
        parser = OptionParser(description = description)
        parser.add_option("-i", "--input",     dest="inputFileName", action="store",                     type="string", help="input file [compulsory] [format: file in mapping format given by -f]")
        parser.add_option("-f", "--format",    dest="format",        action="store",                     type="string", help="format of file [compulsory] [format: mapping file format]")
        parser.add_option("-o", "--output",    dest="output",        action="store",      default=None,  type="string", help="output file [compulsory] [format: output file in GFF3 format]")
        parser.add_option("-v", "--verbosity", dest="verbosity",     action="store",      default=1,     type="int",    help="trace level [format: int]")
        parser.add_option("-G", "--galaxy",    dest="galaxy",        action="store_true", default=False,                help="used for galaxy [format: bool] [default: False]")    
        (options, args) = parser.parse_args()
    
        self.verbosity = options.verbosity
        self.inputFileName = options.inputFileName
        self.format = options.format
        self.output = options.output
        self.galaxy = options.galaxy

    def run(self):  
        if self.verbosity > 0:
            print "Reading input file..."
        parser = TranscriptContainer(self.inputFileName, self.format, self.verbosity)
        if self.verbosity > 0:
            print "... done"
        writer = Gff3Writer(self.output, self.verbosity, self.title)
            
        progress = Progress(parser.getNbTranscripts(), "Reading %s" % (self.inputFileName), self.verbosity)
        for transcript in parser.getIterator():
            writer.addTranscript(transcript)
            progress.inc()
        progress.done()
        
        if self.galaxy:
            os.rename("%s.gff3" % (self.output), self.output) 
            
if __name__ == '__main__':
    launcher = MappingToCoordinates()
    launcher.setAttributesFromCmdLine()
    launcher.run()