view commons/core/parsing/VarscanHit_WithTag.py @ 6:769e306b7933

Change the repository level.

# 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. 
#
# 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.



from commons.core.parsing.VarscanHit import VarscanHit

class VarscanHit_WithTag(VarscanHit):
    
    def __init__(self, tag = "", chrom = "", position = "", ref = "", var = "", readsRef = "", readsVar = "", varFreq = "", strandsRef = "", strandsVar = "", qualRef = "", qualVar = "", pValue = ""):
        self._tag = tag
        VarscanHit.__init__(self, chrom, position, ref, var, readsRef, readsVar, varFreq, strandsRef, strandsVar, qualRef, qualVar, pValue)
        
    def __eq__(self, o):
        if self._tag == o._tag: 
            return VarscanHit.__eq__(self, o)
        return False
    
    def setTag(self, tag):
        self._tag = tag
        
    def getTag(self):
        return self._tag
    
    def getHeader(self):
        return "Chrom\tPosition\tRef\tVar\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\tTag\n"
    
    def getVarscanLine(self):
        return "%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n" % (self.getChrom(), self.getPosition(), self.getRef(), self.getVar(), self.getReadsRef(), self.getReadsVar(), self.getVarFreq(), self.getStrandsRef(), self.getStrandsVar(),  self.getQualRef(), self.getQualVar(), self.getPValue(), self.getTag())
    
    def setAttributes(self, lResults, iCurrentLineNumber):
        VarscanHit.setAttributes(self, lResults, iCurrentLineNumber)
        if lResults[12] != '':
            self.setTag(lResults[12])
            
    def setAttributesFromString(self, varscanString, iCurrentLineNumber ="", fieldSeparator ="\t"):
        varscanString = varscanString.rstrip()
        lvarscanStringItem = varscanString.split(fieldSeparator)
        if len(lvarscanStringItem)<13:
            for i in range(len(lvarscanStringItem), 13):
                lvarscanStringItem.append ("")
        self.setAttributes(lvarscanStringItem, iCurrentLineNumber)