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

Uploaded

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/VarscanHit.py	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,175 @@
+# 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
+
+class VarscanHit(object):
+    
+    def __init__(self, chrom = "", position = "", ref = "", var = "", readsRef = "", readsVar = "", varFreq = "", strandsRef = "", strandsVar = "", qualRef = "", qualVar = "", pValue = ""):
+        self._chrom = chrom
+        self._position = position
+        self._ref = ref
+        self._var = var
+        self._readsRef = readsRef
+        self._readsVar = readsVar
+        self._varFreq = varFreq
+        self._strandsRef = strandsRef
+        self._strandsVar = strandsVar
+        self._qualRef = qualRef
+        self._qualVar = qualVar
+        self._pValue = pValue
+        
+    ## Equal operator
+    #
+    # @param o a VarscanFileAnalysis instance
+    #    
+    def __eq__(self, o):
+        return self._chrom == o._chrom and self._position == o._position and self._ref == o._ref and self._var == o._var
+
+    def setChrom(self, chromosome):
+        self._chrom = chromosome
+    
+    def setPosition(self, position):
+        self._position = position
+    
+    def setRef(self, referenceAllele):
+        self._ref = referenceAllele
+    
+    def setVar(self, variantAllele):
+        self._var = variantAllele
+    
+    def setReadsRef(self, readsRef):
+        self._readsRef = readsRef
+    
+    def setReadsVar(self, readsVar):
+        self._readsVar = readsVar
+        
+    def setVarFreq(self, varFreq):
+        self._varFreq = varFreq
+        
+    def setStrandsRef(self, strandsRef):
+        self._strandsRef = strandsRef
+        
+    def setStrandsVar(self, strandsVar):
+        self._strandsVar = strandsVar
+        
+    def setQualRef(self, qualRef):
+        self._qualRef = qualRef
+        
+    def setQualVar(self, qualVar):
+        self._qualVar = qualVar
+        
+    def setPValue(self, pValue):
+        self._pValue = pValue
+    
+    def getChrom(self):
+        return self._chrom
+    
+    def getPosition(self):
+        return self._position
+    
+    def getRef(self):
+        return self._ref
+    
+    def getVar(self):
+        return self._var
+    
+    def getReadsRef(self):
+        return self._readsRef
+    
+    def getReadsVar(self):
+        return self._readsVar
+    
+    def getVarFreq(self):
+        return self._varFreq
+    
+    def getStrandsRef(self):
+        return self._strandsRef
+    
+    def getStrandsVar(self):
+        return self._strandsVar
+    
+    def getQualRef(self):
+        return self._qualRef
+    
+    def getQualVar(self):
+        return self._qualVar
+    
+    def getPValue(self):
+        return self._pValue
+    
+    def getHeader(self):
+        return "Chrom\tPosition\tRef\tVar\tReads1\tReads2\tVarFreq\tStrands1\tStrands2\tQual1\tQual2\tPvalue\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\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())
+    
+    def setAttributes(self, lResults, iCurrentLineNumber):
+        if lResults[0] != '':
+            self.setChrom(lResults[0])
+        else:
+            raise CheckerException ("The field Chrom is empty in varscan file in line %s" % iCurrentLineNumber)
+        if lResults[1] != '':
+            self.setPosition(lResults[1])
+        else:
+            raise CheckerException ("The field Position is empty in varscan file in line %s" % iCurrentLineNumber)
+        if lResults[2] != '':
+            self.setRef(lResults[2])
+        else:
+            raise CheckerException ("The field Ref is empty in varscan file in line %s" % iCurrentLineNumber)
+        if lResults[3] != '':
+            self.setVar(lResults[3])
+        else:
+            raise CheckerException ("The field Var is empty in varscan file in line %s" % iCurrentLineNumber)
+        if lResults[4] != '':
+            self.setReadsRef(lResults[4])
+        if lResults[5] != '':
+            self.setReadsVar(lResults[5])
+        if lResults[6] != '':
+            self.setVarFreq(lResults[6])
+        if lResults[7] != '':
+            self.setStrandsRef(lResults[7])
+        if lResults[8] != '':
+            self.setStrandsVar(lResults[8])
+        if lResults[9] != '':
+            self.setQualRef(lResults[9])
+        if lResults[10] != '':
+            self.setQualVar(lResults[10])
+        if lResults[11] != '':
+            self.setPValue(lResults[11])
+            
+    def setAttributesFromString(self, varscanString, iCurrentLineNumber ="", fieldSeparator ="\t"):
+        varscanString = varscanString.rstrip()
+        lvarscanStringItem = varscanString.split(fieldSeparator)
+        if len(lvarscanStringItem)<12:
+            for i in range(len(lvarscanStringItem), 12):
+                lvarscanStringItem.append ("")
+        self.setAttributes(lvarscanStringItem, iCurrentLineNumber)
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