--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/VarscanToVCF.py	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,152 @@
+#!/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. 
+#
+# 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.
+
+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()        
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