diff commons/core/parsing/VarscanHitForGnpSNP.py @ 38:2c0c0a89fad7

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/VarscanHitForGnpSNP.py	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,232 @@
+# 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.checker.CheckerException import CheckerException
+from commons.core.parsing.VarscanHit import VarscanHit
+import re
+
+class VarscanHitForGnpSNP(VarscanHit):
+    
+    def __init__(self):
+        VarscanHit.__init__(self)
+        self._reads1 = ''
+        self._reads2 = ''
+        self._varFreq = ''
+        self._strands1 = ''
+        self._strands2 = ''
+        self._qual1 = ''
+        self._qual2 = ''
+        self._pvalue = ''
+        self._5flank = ''
+        self._3flank = ''
+        self._gnpSnp_ref = ''
+        self._gnpSnp_var = ''
+        self._gnpSnp_position = 0
+        self._polymType = ''
+        self._polymLength = 0
+        self._occurrence = 1
+        
+    ## Equal operator
+    #
+    # @param o a VarscanFileAnalysis instance
+    #    
+    def __eq__(self, o):
+        return VarscanHit.__eq__(self, o) \
+             and self._reads1 == o._reads1 and self._reads2 == o._reads2 \
+             and self._varFreq == o._varFreq and self._strands1 == o._strands1 \
+             and self._strands2 == o._strands2 and self._qual1 == o._qual1 \
+             and self._qual2 == o._qual2 and self._pvalue == o._pvalue \
+             and self._3flank == o._3flank and self._5flank == o._5flank \
+             and self._gnpSnp_position == o._gnpSnp_position and self._gnpSnp_ref == o._gnpSnp_ref \
+             and self._gnpSnp_var == o._gnpSnp_var and self._polymLength == o._polymLength \
+             and self._polymType == o._polymType and self._occurrence == o._occurrence
+    
+    def isPolymTypeAlreadyFoundAtThisChromAndThisPosition(self, iVarscanHitForGnpSNP):
+        return self._chrom == iVarscanHitForGnpSNP.getChrom() \
+            and self._position == iVarscanHitForGnpSNP.getPosition() \
+            and self._polymType == iVarscanHitForGnpSNP.getPolymType()
+            
+    def manageOccurrence(self, iVarscanHitForGnpSNP=None):
+        if iVarscanHitForGnpSNP != None and self.isPolymTypeAlreadyFoundAtThisChromAndThisPosition(iVarscanHitForGnpSNP):
+            self._occurrence = iVarscanHitForGnpSNP.getOccurrence() + 1
+    
+    def formatAlleles2GnpSnp(self):
+        if self.getVar().find("-") != -1:
+            self._polymType = "DELETION"
+            self._gnpSnp_position = int(self._position) + 1
+            self._gnpSnp_ref = self._var[1:]
+            self._gnpSnp_var = "-" * len(self._gnpSnp_ref)
+            self._polymLength = len(self._gnpSnp_ref)
+        elif self.getVar().find("+") != -1:
+            self._polymType = "INSERTION"
+            self._gnpSnp_position = int(self._position)
+            self._gnpSnp_var = self._var[1:]
+            self._gnpSnp_ref = "-" * len(self._gnpSnp_var)
+            self._polymLength = 1
+        else:
+            self._polymType = "SNP"
+            self._gnpSnp_position = int(self._position)
+            self._gnpSnp_var = self._var
+            self._gnpSnp_ref = self._ref
+            self._polymLength = 1
+    
+    def setReads1(self, nbReadsLikeRef):
+        self._reads1 = nbReadsLikeRef
+    
+    def setReads2(self, nbReadsLikeVar):
+        self._reads2 = nbReadsLikeVar
+    
+    def setVarFreq(self, frequencyOfVariantAllele):
+        frequencyOfVariantAllele = frequencyOfVariantAllele.replace("%","")
+        frequencyOfVariantAllele = frequencyOfVariantAllele.replace(",",".")
+        self._varFreq = float(frequencyOfVariantAllele)
+    
+    def setStrands1(self, strandsOfReferenceAllele):
+        self._strands1 = strandsOfReferenceAllele
+    
+    def setStrands2(self, strandsOfVariantAllele):
+        self._strands2 = strandsOfVariantAllele
+    
+    def setQual1(self, averageQualityOfRef):
+        self._qual1 = averageQualityOfRef
+    
+    def setQual2(self, averageQualityOfVar):
+        self._qual2 = averageQualityOfVar
+    
+    def setPvalue(self, pvalue):
+        self._pvalue = pvalue
+    
+    def set5flank(self, s5flank):
+        self._5flank = s5flank
+    
+    def set3flank(self, s3flank):
+        self._3flank = s3flank
+        
+    def setGnpSNPRef(self, ref):
+        self._gnpSnp_ref = ref
+        
+    def setGnpSNPVar(self, var):
+        self._gnpSnp_var = var
+        
+    def setGnpSNPPosition(self, position):
+        self._gnpSnp_position = position
+    
+    def setOccurrence(self, occurrence):
+        self._occurrence = occurrence
+        
+    def setPolymType(self, polymType):
+        self._polymType = polymType
+        
+    def setPolymLength(self, polymLength):
+        self._polymLength = polymLength
+    
+    def getReads1(self):
+        return self._reads1
+    
+    def getReads2(self):
+        return self._reads2
+    
+    def getVarFreq(self):
+        return self._varFreq
+    
+    def getStrands1(self):
+        return self._strands1
+    
+    def getStrands2(self):
+        return self._strands2
+    
+    def getQual1(self):
+        return self._qual1
+    
+    def getQual2(self):
+        return self._qual2
+    
+    def getPvalue(self):
+        return self._pvalue
+    
+    def get5flank(self):
+        return self._5flank
+    
+    def get3flank(self):
+        return self._3flank
+    
+    def getPolymType(self):
+        return self._polymType
+    
+    def getGnpSnpVar(self):
+        return self._gnpSnp_var
+    
+    def getGnpSnpRef(self):
+        return self._gnpSnp_ref
+    
+    def getGnpSnpPosition(self):
+        return self._gnpSnp_position
+    
+    def getPolymLength(self):
+        return self._polymLength
+    
+    def getOccurrence(self):
+        return self._occurrence
+    
+    def setAttributes(self, lResults, iCurrentLineNumber):
+        VarscanHit.setAttributes(self, lResults, iCurrentLineNumber)
+        if lResults[4] != '':
+            self.setReads1(lResults[4])
+        else:
+            raise CheckerException ("The field Reads1 is empty in varscan file in line %s" % (iCurrentLineNumber))
+        if lResults[5] != '':
+            self.setReads2(lResults[5])
+        else:
+            raise CheckerException ("The field Reads2 is empty in varscan file in line %s" % (iCurrentLineNumber))
+        if lResults[6] != '' and re.match("[0-9\,\%]+", lResults[6]):
+            self.setVarFreq(lResults[6])
+        else:
+            raise CheckerException ("The field VarFreq is empty or in bad format in varscan file in line %s" % (iCurrentLineNumber))
+        if lResults[7] != '':
+            self.setStrands1(lResults[7])
+        else:
+            raise CheckerException ("The field Strands1 is empty in varscan file in line %s" % (iCurrentLineNumber))
+        if lResults[8] != '':
+            self.setStrands2(lResults[8])
+        else:
+            raise CheckerException ("The field Strands2 is empty in varscan file in line %s" % (iCurrentLineNumber))
+        if lResults[9] != '':
+            self.setQual1(lResults[9])
+        else:
+            raise CheckerException ("The field Qual1 is empty in varscan file in line %s" % (iCurrentLineNumber))
+        if lResults[10] != '':
+            self.setQual2(lResults[10])
+        else:
+            raise CheckerException ("The field Qual2 is empty in varscan file in line %s" % (iCurrentLineNumber))
+        if lResults[11] != '':
+            self.setPvalue(lResults[11])
+        else:
+            raise CheckerException ("The field Pvalue is empty in varscan file in line %s" % (iCurrentLineNumber))
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