--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/commons/core/parsing/VarscanFileForGnpSNP.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,72 @@
+# 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.VarscanHitForGnpSNP import VarscanHitForGnpSNP
+from commons.core.parsing.VarscanFile import VarscanFile
+
+class VarscanFileForGnpSNP(VarscanFile):
+    
+    def __init__(self, varscanFileName, fastqFileName="", refFastaFileName="", taxonName=""):
+        VarscanFile.__init__(self, varscanFileName)
+        self._fastqFileName = fastqFileName
+        self._refFastaFileName = refFastaFileName
+        self._taxonName = taxonName
+        self._previousVarscanHit = None
+        
+    ## Equal operator
+    #
+    # @param o a VarscanFileAnalysis instance
+    #    
+    def __eq__(self, o):
+        return VarscanFile.__eq__(self, o) and self._fastqFileName == o._fastqFileName \
+            and self._refFastaFileName == o._refFastaFileName and self._taxonName == o._taxonName
+             
+    def getVarscanFieldSeparator(self):
+        return self._varscanFieldSeparator
+        
+    def getFastqFileName(self):
+        return self._fastqFileName
+    
+    def getRefFastaFileName(self):
+        return self._refFastaFileName
+    
+    def getTaxonName(self):
+        return self._taxonName
+        
+    def createVarscanHit(self, line, currentLineNumber):
+        line = line.strip()
+        lResults = line.split(self._varscanFieldSeparator)
+        iVarscanHit = VarscanHitForGnpSNP()
+        iVarscanHit.setAttributes(lResults, currentLineNumber)
+        iVarscanHit.formatAlleles2GnpSnp()
+        iVarscanHit.manageOccurrence(self._previousVarscanHit)
+        self._previousVarscanHit = iVarscanHit
+        return iVarscanHit