--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/NucmerParser.py	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,88 @@
+#
+# 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.SubMapping import SubMapping
+from SMART.Java.Python.structure.Mapping import Mapping
+from SMART.Java.Python.structure.Interval import Interval
+from commons.core.parsing.MapperParser import MapperParser
+
+
+class NucmerParser(MapperParser):
+    """A class that parses the output of Nucmer"""
+
+    def __init__(self, fileName, verbosity = 0):
+        super(NucmerParser, self).__init__(fileName, verbosity)
+
+
+    def __del__(self):
+        super(NucmerParser, self).__del__()
+
+
+    def getFileFormats():
+        return ["nucmer"]
+    getFileFormats = staticmethod(getFileFormats)
+
+
+    def skipFirstLines(self):
+        pass
+
+
+    def parseLine(self, line):
+        if not line:
+            return None
+        if line[0] == ">":
+            self.currentChromosome = line[1:].split()[0]
+            return None
+        splittedLine = line.strip().split()
+        if len(splittedLine) != 8:
+            raise Exception("Line %d '%s' does not have a NucMer format" % (self.currentLineNb, line))
+
+        subMapping = SubMapping()
+
+        subMapping.targetInterval.setChromosome(self.currentChromosome)
+        subMapping.targetInterval.setName(self.currentChromosome)
+        subMapping.targetInterval.setStart(min(int(splittedLine[0]), int(splittedLine[1])))
+        subMapping.targetInterval.setEnd(max(int(splittedLine[0]), int(splittedLine[1])))
+        subMapping.targetInterval.setDirection(splittedLine[6])
+
+        subMapping.queryInterval.setChromosome(splittedLine[7])
+        subMapping.queryInterval.setName(splittedLine[7])
+        subMapping.queryInterval.setStart(1)
+        subMapping.queryInterval.setEnd(int(splittedLine[3]))
+        subMapping.queryInterval.setDirection("+")
+
+        mapping = Mapping()
+        mapping.addSubMapping(subMapping)
+        mapping.setDirection(splittedLine[6])
+        mapping.setIdentity(float(splittedLine[5]))
+        mapping.setSize(int(splittedLine[3]))
+
+        return mapping