--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/SsrParser.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,170 @@
+# 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 sys
+
+## this class can parse a Ssr results output file. SSR.pl is developped by S.Cartinhour. (5/2000)
+#
+class SsrParser(object):
+
+
+    def __init__(self, BES_name='', BES_redundancy='', SSR_nbNucleotides='', SSR_Motif='', SSR_Motif_number='', SSR_start='', SSR_end='', BES_size=''):
+        self._BesName = BES_name
+        self._BesRedundancy = BES_redundancy
+        self._SsrNbNucleotides = SSR_nbNucleotides
+        self._SsrMotif = SSR_Motif
+        self._SsrMotifNumber = SSR_Motif_number
+        self._SsrStart = SSR_start
+        self._SsrEnd = SSR_end
+        self._BesSize = BES_size
+        
+    def __eq__(self, o):
+        return self._BesName == o._BesName and self._BesRedundancy == o._BesRedundancy and self._SsrNbNucleotides == o._SsrNbNucleotides and self._SsrMotif == o._SsrMotif and self._SsrMotifNumber == o._SsrMotifNumber and self._SsrStart == o._SsrStart and self._SsrEnd == o._SsrEnd and self._BesSize == o._BesSize
+        
+    def setBesName(self, BES_Name):
+        self._BesName = BES_Name
+        
+    def setBesRedundancy(self, BES_redundancy):
+        self._BesRedundancy = BES_redundancy
+        
+    def setSsrNbNucleotides(self, SSR_nbNucleotides):
+        self._SsrNbNucleotides = SSR_nbNucleotides
+        
+    def setSsrMotif(self, SSR_Motif):
+        self._SsrMotif = SSR_Motif
+        
+    def setSsrMotifNumber(self, SSR_Motif_number):
+        self._SsrMotifNumber = SSR_Motif_number
+        
+    def setSsrStart(self, SSR_start):
+        self._SsrStart = SSR_start
+        
+    def setSsrEnd(self, SSR_end):
+        self._SsrEnd = SSR_end
+        
+    def setBesSize(self, BES_size):
+        self._BesSize = BES_size
+        
+    def getBesName(self):
+        return self._BesName
+        
+    def getBesRedundancy(self):
+        return self._BesRedundancy
+        
+    def getSsrNbNucleotides(self):
+        return self._SsrNbNucleotides
+        
+    def getSsrMotif(self):
+        return self._SsrMotif
+        
+    def getSsrMotifNumber(self):
+        return self._SsrMotifNumber
+        
+    def getSsrStart(self):
+        return self._SsrStart
+        
+    def getSsrEnd(self):
+        return self._SsrEnd
+        
+    def getBesSize(self):
+        return self._BesSize
+    
+    def setAttributes(self, lResults, iCurrentLineNumber):
+        error = False
+        
+        if lResults[0] != '':
+            self.setBesName(lResults[0])
+        else:
+            sys.stderr.write("WARNING: The field BES Name is empty in SSR results file in line %s\n" % iCurrentLineNumber)
+            error = True
+        
+        if lResults[1] != '':
+            self.setBesRedundancy(lResults[1])
+        else:
+            sys.stderr.write("WARNING: The field BES Redundancy is empty in SSR results file in line %s\n" % iCurrentLineNumber)
+            error = True
+        
+        if lResults[2] != '':
+            self.setSsrNbNucleotides(lResults[2])
+        else:
+            sys.stderr.write("WARNING: The field SSR Number Nucleotides is empty in SSR results file in line %s\n" % iCurrentLineNumber)
+            error = True
+    
+        if lResults[3] != '':
+            self.setSsrMotif(lResults[3])
+        else:
+            sys.stderr.write("WARNING: The field SSR Motif is empty in SSR results file in line %s\n" % iCurrentLineNumber)
+            error = True
+    
+        if lResults[4] != '':
+            self.setSsrMotifNumber(lResults[4])
+        else:
+            sys.stderr.write("WARNING: The field SSR Motif Number is empty in SSR results file in line %s\n" % iCurrentLineNumber)
+            error = True
+    
+        if lResults[5] != '':
+            self.setSsrStart(lResults[5])
+        else:
+            sys.stderr.write("WARNING: The field SSR Start is empty in SSR results file in line %s\n" % iCurrentLineNumber)
+            error = True
+    
+        if lResults[6] != '':
+            self.setSsrEnd(lResults[6])
+        else:
+            sys.stderr.write("WARNING: The field SSR End is empty in SSR results file in line %s\n" % iCurrentLineNumber)
+            error = True
+    
+        if lResults[7] != '':
+            self.setBesSize(lResults[7])
+        else:
+            sys.stderr.write("WARNING: The field BES Size is empty in SSR results file in line %s\n" % iCurrentLineNumber)
+            error = True
+            
+        if error == True:
+            self._setAllToNull()
+            
+    def setAttributesFromString(self, ssrLine, iCurrentLineNumber ="", fieldSeparator ="\t"):
+        ssrLine = ssrLine.rstrip()
+        lSsrLineItem = ssrLine.split(fieldSeparator)
+        if len(lSsrLineItem) < 8:
+            sys.stderr.write("WARNING: The line %s is not a valid SSR Result line\n" % iCurrentLineNumber)
+        else:
+            self.setAttributes(lSsrLineItem, iCurrentLineNumber)
+            
+    def _setAllToNull(self):
+        self._BesName = ''
+        self._BesRedundancy = ''
+        self._SsrNbNucleotides = ''
+        self._SsrMotif = ''
+        self._SsrMotifNumber = ''
+        self._SsrStart = ''
+        self._SsrEnd = ''
+        self._BesSize = ''
+    
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