--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/CrossSsrAndBesMappedByBlatToGff.py	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,197 @@
+# 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 os
+import optparse
+from commons.core.parsing.SsrParser import SsrParser
+from commons.core.parsing.BlatParser import BlatParser
+
+class CrossSsrAndBesMappedByBlatToGff(object):
+
+
+    def __init__(self):
+        self._inputFileSSR = ''
+        self._inputFileBlat = ''
+        self._outputFileGFF = ''
+    
+    def setAttributesFromCmdLine(self):
+        help = '\
+        \nThis Script Launch CrossSsrAndBesMappedByBlatToGff.\n\n\
+        Example 1: python CrossSsrAndBesMappedByBlatToGff.py -s ssrResultsFile.tab -b blatResultsFile.tab -o outputFile.gff3\n\
+        Example 2: python CrossSsrAndBesMappedByBlatToGff.py -s ssrResultsFile.tab -b blatResultsFile.tab -o outputFile.gff3 -n muscadine:filtre1\n\n'
+        
+        parser = optparse.OptionParser(usage= help, version="CovertSamToFastq.py v1.0")
+        parser.add_option( '-s', '--ssr', dest='inputSSR', help='SSR Input File Name [Format: tabular]', default= None )
+        parser.add_option( '-b', '--blat', dest='inputBLAT', help='Blat Input File Name [Format: tabular]', default= None )
+        parser.add_option( '-o', '--output', dest='output', help='Output File Name [Format: GFF3]', default= None )
+        parser.add_option( '-n', '--methodName', dest='methodName', help='Method name in col. 3 [Default: None]', default= None )
+        ( options, args ) = parser.parse_args()
+        self.options = options
+    
+    def checkOptions(self):
+        if self.options.inputSSR == '':
+            raise Exception("ERROR: No SSR file specified for -s !")
+        elif not os.path.exists(self.options.inputSSR):
+            raise Exception("ERROR: SSR Input File doesn't exist !")
+        else:
+            self._inputFileSSR = self.options.inputSSR
+        
+        if self.options.inputBLAT == '':
+            raise Exception("ERROR: No Blat file specified for -b !")
+        elif not os.path.exists(self.options.inputBLAT):
+            raise Exception("ERROR: Blat Input File doesn't exist !")
+        else:
+            self._inputFileBlat = self.options.inputBLAT
+            
+        if self.options.output == '':
+            raise Exception("ERROR: No Output file specified for -o !")
+        else:
+            self._outputFileGFF = self.options.output
+            
+        self._methodName = self.options.methodName
+    
+    def run(self):
+        self.checkOptions()
+        self._createGFFOutputFile()
+        
+        dictSsrParser = {}
+        dictSsrParser = self.createDictOfSsrParser(dictSsrParser)
+        
+        BLATFile = open(self._inputFileBlat, 'r')
+        
+        headerBlatLine = BLATFile.readline()
+        headerBlatLine = BLATFile.readline()
+        headerBlatLine = BLATFile.readline()
+        headerBlatLine = BLATFile.readline()
+        headerBlatLine = BLATFile.readline()
+        blatLine = BLATFile.readline()
+        numberLine = 6
+        while blatLine != '' and blatLine != '\n':
+            thisBlatHit = BlatParser()
+            thisBlatHit.setAttributesFromString(blatLine, numberLine)
+            besName = thisBlatHit.getQName()
+            
+            if besName in dictSsrParser:
+                lLinesToPrint = self.createListOfGFFLinesForThisBesWithSSR(thisBlatHit, dictSsrParser)
+                self._printGFFLinesToOutputFile(lLinesToPrint)
+            
+            blatLine = BLATFile.readline()
+            numberLine = numberLine + 1
+        
+        BLATFile.close()
+        
+    def createDictOfSsrParser(self, dictSsrParser):
+        dictSsrParser = {}
+        SSRFile = open(self._inputFileSSR, 'r')
+        
+        header = SSRFile.readline()
+        line = SSRFile.readline()
+        numberLine = 2
+        
+        while line != '' and line != '\n':
+            thisSSRHit = SsrParser()
+            thisSSRHit.setAttributesFromString(line, numberLine)
+            
+            BESName = thisSSRHit.getBesName()
+            if not BESName in dictSsrParser:
+                list = [thisSSRHit]
+                dictSsrParser[BESName] = list
+            else:
+                list = dictSsrParser[BESName]
+                list.append(thisSSRHit)
+                dictSsrParser[BESName] = list
+            
+            line = SSRFile.readline()
+            numberLine = numberLine + 1
+            
+        SSRFile.close()
+        return dictSsrParser
+    
+    def createListOfGFFLinesForThisBesWithSSR(self, BlatHitObject, dictSsrParser):
+        listGffLines = []
+        
+        besNameToKeep =  BlatHitObject.getQName()
+        lOfSSRHitObject = dictSsrParser[besNameToKeep]
+        
+        for SSRHitObject in  lOfSSRHitObject:
+            posSSRStart = self.convertSSRPositionsToChromPositions(SSRHitObject.getSsrStart(), BlatHitObject.getTStart(), BlatHitObject.getTEnd(), BlatHitObject.getStrand())
+            posSSREnd = self.convertSSRPositionsToChromPositions(SSRHitObject.getSsrEnd(), BlatHitObject.getTStart(), BlatHitObject.getTEnd(), BlatHitObject.getStrand())
+            ssrSeq = self.getSsrSeq(SSRHitObject.getSsrMotif(), SSRHitObject.getSsrMotifNumber())
+            
+            col1 = BlatHitObject.getTName()
+            col2 = 'CrossSsrAndBesAlignedByBlat'
+            if self._methodName != '' and self._methodName != None:
+                col3 = '%s:SSR' %self._methodName
+            else:
+                col3 = 'SSR'
+            col4 = posSSRStart
+            col5 = posSSREnd
+            col6 = '.'
+            col7 = BlatHitObject.getStrand()
+            col8 = '.'
+            col9 = 'ID=SSR_%s_%s;Name=SSR_%s_%s;bes_name=%s;bes_size=%s;bes_matchstart=%s;bes_matchend=%s;bes_redundancy=%s;ssr_type=%s;ssr_motif=%s;ssr_motif_number=%s;ssr_start=%s;ssr_end=%s;muscadine_seq=%s' % (besNameToKeep, SSRHitObject.getBesRedundancy(), 
+                                                                                                                                                                                           besNameToKeep, SSRHitObject.getBesRedundancy(),
+                                                                                                                                                                                           besNameToKeep, BlatHitObject.getQSize(),
+                                                                                                                                                                                           BlatHitObject.getQStart(), BlatHitObject.getQEnd(), 
+                                                                                                                                                                                           SSRHitObject.getBesRedundancy(), SSRHitObject.getSsrNbNucleotides(),
+                                                                                                                                                                                           SSRHitObject.getSsrMotif(), SSRHitObject.getSsrMotifNumber(),
+                                                                                                                                                                                           SSRHitObject.getSsrStart(), SSRHitObject.getSsrEnd(), ssrSeq)
+            gffLine = '%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%s\n' % (col1, col2, col3, col4, col5, col6, col7, col8, col9)
+            listGffLines.append(gffLine)
+            
+        return listGffLines
+    
+    def convertSSRPositionsToChromPositions(self, ssrPos, chromPosStart, chromPosEnd, strand):
+        if strand == '+':
+            newPos =  int(chromPosStart) + int(ssrPos) - 1
+        elif strand == '-':
+            newPos =  int(chromPosEnd) - int(ssrPos) + 1
+        return newPos
+    
+    def getSsrSeq(self, motif, nbMotif):
+        ssrSeq = motif * int(nbMotif)
+        return ssrSeq
+    
+    def _createGFFOutputFile(self):
+        GFFfile = open(self._outputFileGFF, 'w')
+        GFFfile.write("##gff-version 3\n")
+        GFFfile.close()
+        
+    def _printGFFLinesToOutputFile(self, lLinesToPrint):
+        GFFfile = open(self._outputFileGFF, 'a')
+        for line in lLinesToPrint:
+            GFFfile.write(line)
+        GFFfile.close()
+
+if __name__ == '__main__':
+    iCrossSsrAndBesMappedByBlatToGff = CrossSsrAndBesMappedByBlatToGff()
+    iCrossSsrAndBesMappedByBlatToGff.setAttributesFromCmdLine()
+    iCrossSsrAndBesMappedByBlatToGff.run()
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