view commons/core/parsing/VarscanToVCF.py @ 18:94ab73e8a190

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#!/usr/bin/env python

# Copyright INRA (Institut National de la Recherche Agronomique)
# http://www.inra.fr
# http://urgi.versailles.inra.fr
#
# 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. 
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# 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
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# same conditions as regards security. 
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import math
from commons.core.LoggerFactory import LoggerFactory
from commons.core.utils.RepetOptionParser import RepetOptionParser
from commons.core.utils.FileUtils import FileUtils
from commons.core.parsing.VarscanFile import VarscanFile
from commons.core.seq.Bioseq import Bioseq

LOG_DEPTH = "core.parsing"

##Reference launcher implementation
#
class VarscanToVCF(object):
    
    def __init__(self, varscanFileName = "", vcfFileName = "", doClean = False, verbosity = 0):
        self._varscanFileName = varscanFileName
        self.setvcfFileName(vcfFileName)
        self._doClean = doClean
        self._verbosity = verbosity
        
        self._vcfRevision = "VCFv4.1"
        self._vcfHeader = "#CHROM\tPOS\tID\tREF\tALT\tQUAL\tFILTER\tINFO"
        
        self._log = LoggerFactory.createLogger("%s.%s" % (LOG_DEPTH, self.__class__.__name__), self._verbosity)
        
    def setAttributesFromCmdLine(self):
        description = "Conver Varscan file to VCF file."
        epilog = "\t$ python VarscanToVCF.py -i varscanFileName -v 2"
        parser = RepetOptionParser(description = description, epilog = epilog)
        parser.add_option("-i", "--Varscan",    dest = "varscanFileName", action = "store",       type = "string", help = "input Varscan file name [compulsory] [format: varscan2.2.8]", default = "")
        parser.add_option("-o", "--vcfFileName",dest = "vcfFileName",     action = "store",       type = "string", help = "vcfFileName file name [default: <input>.vcf]", default = "")
        parser.add_option("-c", "--clean",      dest = "doClean",         action = "store_true",                   help = "clean temporary files [optional] [default: False]", default = False)
        parser.add_option("-v", "--verbosity",  dest = "verbosity",       action = "store",       type = "int",    help = "verbosity [optional] [default: 1]", default = 1)
        options = parser.parse_args()[0]
        self._setAttributesFromOptions(options)
        
    def _setAttributesFromOptions(self, options):
        self.setvarscanFileName(options.varscanFileName)
        self.setvcfFileName(options.vcfFileName)
        self.setDoClean(options.doClean)
        self.setVerbosity(options.verbosity)

    def setvarscanFileName(self, varscanFileName):
        self._varscanFileName = varscanFileName
        
    def setvcfFileName(self, vcfFileName):
        if vcfFileName == "":
            self._vcfFileName = "%s.vcf" % self._varscanFileName
        else:
            self._vcfFileName = vcfFileName
        
    def setDoClean(self, doClean):
        self._doClean = doClean
        
    def setVerbosity(self, verbosity):
        self._verbosity = verbosity
        
    def _checkOptions(self):
        if self._varscanFileName == "":
            self._logAndRaise("ERROR: Missing input file name")
        else:
            if not FileUtils.isRessourceExists(self._varscanFileName):
                self._logAndRaise("ERROR: Input Varscan file '%s' does not exist!" % self._varscanFileName)
            
    def _logAndRaise(self, errorMsg):
        self._log.error(errorMsg)
        raise Exception(errorMsg)

    def _convertVarscanLineToVCFRecord(self, varscanLine, lineNumber):
        iVarscanFile = VarscanFile()
        iVarscanFile.setTypeOfVarscanFile("Varscan_2_2_8")
        iVarscanHit = iVarscanFile.createVarscanObjectFromLine(varscanLine, lineNumber)
        Chrom = iVarscanHit.getChrom()
        Pos = int(iVarscanHit.getPosition())
        #ID = str(lineNumber)
        ID = "."
        Ref = iVarscanHit.getRef()
        Alt = iVarscanHit.getVar()
        Qual = -10*math.log10(float(iVarscanHit.getPValue()))
        Filter = "."
        AF = float(iVarscanHit.getVarFreq()[:-1])/100
        DP = int(iVarscanHit.getReadsRef()) + int(iVarscanHit.getReadsVar())
        RBQ = iVarscanHit.getQualRef()
        ABQ = iVarscanHit.getQualVar()
        #MQ = iVarscanHit.getMapQualRef()
        Info = ";".join(["AF=%.4f" %AF,"DP=%d" %DP,"RBQ=%s" %RBQ, "ABQ=%s" %ABQ])

        allel = Bioseq().getATGCNFromIUPACandATGCN(iVarscanHit.getCns(), Ref)
        if allel != Alt:
            self._log.warning("'VarAllele' attribute of Varscan file line '%d' was not correct. Correcting using '%s' instead of '%s'." % (lineNumber, allel, Alt))
            Alt = allel
        
        vcfLine = "%s\t%s\t%s\t%s\t%s\t%.9f\t%s\t%s\n" % (Chrom, Pos, ID, Ref, Alt, Qual, Filter, Info)
        return vcfLine

    def run(self):
        LoggerFactory.setLevel(self._log, self._verbosity)
        self._checkOptions()
        self._log.info("START Varscan To VCF")
        self._log.debug("Input file name: %s" % self._varscanFileName)
        
        with open(self._vcfFileName, "w") as fVCF:
            fVCF.write("##fileformat=%s\n" % self._vcfRevision)
            fVCF.write("%s\n" % self._vcfHeader)
            
            with open(self._varscanFileName, "r") as fVarscan:
                lineNumber = 1
                line = fVarscan.readline()
                while line:
                    if line[0] != "#" and "Chrom\tPosition\tRef\tCons" not in line:
                        vcfLine = self._convertVarscanLineToVCFRecord(line, lineNumber)
                        fVCF.write(vcfLine)
                    line = fVarscan.readline()
                    lineNumber += 1
        
        self._log.info("END Varscan To VCF")

if __name__ == "__main__":
    iLaunch = VarscanToVCF()
    iLaunch.setAttributesFromCmdLine()
    iLaunch.run()