annotate smart_toolShed/SMART/Java/Python/mergeTranscriptLists.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
# 
# 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
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# "http://www.cecill.info".
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"""Merge elements of two transcript lists with some condition"""

import os, random, shutil, glob
from optparse import OptionParser
from commons.core.parsing.SequenceListParser import SequenceListParser
from commons.core.parsing.BedParser import BedParser
from commons.core.parsing.GffParser import GffParser
from commons.core.writer.TranscriptWriter import TranscriptWriter
from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
from SMART.Java.Python.misc.RPlotter import RPlotter
from SMART.Java.Python.misc.Progress import Progress



class MergeLists(object):

    def __init__(self, verbosity):
        self.verbosity     = verbosity
        self.seed          = random.randint(0, 100000)
        self.aggregation   = False
        self.normalization = False
        self.distance      = False
        self.antisense     = False
        self.colinear      = False
        self.fileNames     = {}
        self.formats       = {}
        self.tmpFileNames  = []
        self.logHandle     = None

#    def __del__(self):
#        for fileNameRoot in self.tmpFileNames:
#            for fileName in glob.glob("%s*" % (fileNameRoot)):
#                os.remove(fileName)
#        if self.logHandle != None:
#            self.logHandle.close()
#            self.logHandle = None

    def setLogFileName(self, fileName):
        self.logHandle = open(fileName, "w")

    def setInputFileName(self, fileName, format, id):
        self.fileNames[id] = fileName
        self.formats[id]   = format

    def setOutputFileName(self, fileName):
        self.outputFileName = fileName

    def setAggregate(self, aggregation):
        self.aggregation = aggregation

    def setNormalization(self, normalization):
        self.normalization = normalization

    def setDistance(self, distance):
        self.distance = distance

    def setAntisense(self, antisense):
        self.antisense = antisense

    def setColinear(self, colinear):
        self.colinear = colinear

    def createTmpFileName(self, root):
        fileName = "tmp_%s_%d.gff3" % (root, self.seed)
        self.tmpFileNames.append(fileName)
        return fileName

    def selfMerge(self, fileName, format, outputFileName):
        transcriptListComparator = TranscriptListsComparator(self.logHandle, self.verbosity)
        transcriptListComparator.getColinearOnly(True)
        transcriptListComparator.setNormalization(self.normalization)
        transcriptContainer = TranscriptContainer(fileName, format, self.verbosity)
        writer              = TranscriptWriter(outputFileName, "gff3", self.verbosity)
        transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.QUERY, transcriptContainer)
        transcriptListComparator.setOutputWriter(writer)
        transcriptListComparator.compareTranscriptListSelfMerge()

    def keepOverlapping(self, fileNames, formats, outputFileName):
        transcriptListComparator = TranscriptListsComparator(self.logHandle, self.verbosity)
        transcriptListComparator.getAntisenseOnly(self.antisense)
        transcriptListComparator.getColinearOnly(self.colinear)
        for i in (0, 1):
            transcriptContainer = TranscriptContainer(fileNames[i], formats[i], self.verbosity)
            transcriptListComparator.setInputTranscriptContainer(i, transcriptContainer)
        transcriptListComparator.aggregate(self.aggregation)
        transcriptListComparator.setNormalization(self.normalization)
        transcriptListComparator.setMaxDistance(self.distance)
        writer = TranscriptWriter(outputFileName, "gff3", self.verbosity)
        transcriptListComparator.setOutputWriter(writer)
        transcriptListComparator.compareTranscriptList()

    def mergeFiles(self, fileName1, fileName2, outputFileName):
        outputFile = open(outputFileName, "w")
        shutil.copyfileobj(open(fileName1, "r"), outputFile)
        shutil.copyfileobj(open(fileName2, "r"), outputFile)
        outputFile.close()

    def run(self):
        selectedFileQuery = self.createTmpFileName("query")
        self.keepOverlapping({0: self.fileNames[0], 1: self.fileNames[0]}, {0: "gff3", 1: "gff3"}, selectedFileQuery)
        mergeFileTarget = self.createTmpFileName("target")
        self.selfMerge(self.fileNames[1], self.formats[1], mergeFileTarget)
        if not self.aggregation:
            overlapFile = self.createTmpFileName("overlap")
            self.keepOverlapping({0: mergeFileTarget, 1: selectedFileQuery}, {0: "gff3", 1: "gff3"}, overlapFile)
            mergeFileTarget = overlapFile
        mergeFileMerged = self.createTmpFileName("merged")
        self.mergeFiles(mergeFileTarget, selectedFileQuery, mergeFileMerged)
        self.selfMerge(mergeFileMerged, "gff3", self.outputFileName)



if __name__ == "__main__":
    
    # parse command line
    description = "Merge Lists v1.0.3: Merge the elements of two lists of genomic coordinates. [Category: Merge]"

    parser = OptionParser(description = description)
    parser.add_option("-i", "--input1",    dest="inputFileName1", action="store",                       type="string", help="input file 1 [compulsory] [format: file in transcript format given by -f]")
    parser.add_option("-f", "--format1",   dest="format1",        action="store",                       type="string", help="format of file 1 [compulsory] [format: transcript file format]")
    parser.add_option("-j", "--input2",    dest="inputFileName2", action="store",      default=None,    type="string", help="input file 2 [compulsory] [format: file in transcript format given by -g]")
    parser.add_option("-g", "--format2",   dest="format2",        action="store",      default=None,    type="string", help="format of file 2 [compulsory] [format: file in transcript format]")
    parser.add_option("-o", "--output",    dest="outputFileName", action="store",      default=None,    type="string", help="output file [compulsory] [format: output file in GFF3 format]")
    parser.add_option("-k", "--all",       dest="all",            action="store_true", default=False,                  help="print all the transcripts, not only those overlapping [format: bool] [default: false]")
    parser.add_option("-d", "--distance",  dest="distance",       action="store",      default=0,       type="int",    help="max. distance between two transcripts [format: int] [default: 0]")
    parser.add_option("-a", "--antisense", dest="antisense",      action="store_true", default=False,                  help="antisense only [format: bool] [default: false]")
    parser.add_option("-c", "--colinear",  dest="colinear",       action="store_true", default=False,                  help="colinear only [format: bool] [default: false]")
    parser.add_option("-n", "--normalize", dest="normalize",      action="store_true", default=False,                  help="normalize the number of reads per cluster by the number of mappings per read [format: bool] [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()

#    ml = MergeLists(logHandle, options.verbosity)
    
    ml = MergeLists(0)
    ml.setInputFileName(options.inputFileName1, options.format1, 0)
    ml.setInputFileName(options.inputFileName2, options.format2, 1)
    ml.setOutputFileName(options.outputFileName)
    ml.setAntisense(options.antisense)
    ml.setColinear(options.colinear)
    ml.setAggregate(options.all)
    ml.setNormalization(options.normalize)
    ml.setDistance(options.distance)
    ml.run()