--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/MapParser.py	Tue Apr 30 15:02:29 2013 -0400
@@ -0,0 +1,67 @@
+#
+# Copyright INRA-URGI 2009-2010
+# 
+# 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 re
+import sys
+from SMART.Java.Python.structure.Mapping import Mapping
+from commons.core.parsing.MapperParser import MapperParser
+from SMART.Java.Python.structure.SubMapping import SubMapping
+from SMART.Java.Python.misc import Utils
+from SMART.Java.Python.structure.Transcript import Transcript
+from commons.core.parsing.TranscriptListParser import TranscriptListParser
+
+
+class MapParser(TranscriptListParser):
+    """A class that parses the repet .map files"""
+
+    def __init__(self, fileName, verbosity = 0):
+        self._lineParseRe = re.compile(r"(?P<seqName>\w+)\s(?P<chrName>\w+)\s(?P<sStart>\d+)\s(?P<sEnd>\d+)")
+        TranscriptListParser.__init__(self, fileName, verbosity)
+
+    def getFileFormats():
+        return ["map"]
+    getFileFormats = staticmethod(getFileFormats)
+
+    def skipFirstLines(self):    
+        return
+        
+    def parseLine(self, line):
+        m = self._lineParseRe.search(line)
+        
+        if m == None:
+            sys.exit("\nLine %d '%s' does not have a map format" % (self.currentLineNb, line))
+            
+        transcript = Transcript()
+        transcript.setChromosome(m.group("chrName"))
+        transcript.setStart(min(int(m.group("sStart")), int(m.group("sEnd"))))
+        transcript.setEnd(max(int(m.group("sStart")), int(m.group("sEnd"))))
+        transcript.setName(m.group("seqName"))
+        transcript.setDirection(1)
+
+        return transcript