--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/ShrimpParser.py	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,107 @@
+#
+# 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
+
+
+class ShrimpParser(MapperParser):
+    """A class that parses the output of Shrimp"""
+
+    def __init__(self, fileName, verbosity = 0):
+        super(ShrimpParser, self).__init__(fileName, verbosity)
+
+
+    def __del__(self):
+        super(ShrimpParser, self).__del__()
+
+
+    def getFileFormats():
+        return ["shrimp"]
+    getFileFormats = staticmethod(getFileFormats)
+
+
+    def skipFirstLines(self):
+        self.handle.readline()
+        self.currentLineNb += 1
+
+
+    def parseLine(self, line):
+        m = re.search(r"^\s*>([^\t]+)\t+(\S+)\s+([+-])\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s*$", line)
+        if m == None:
+            sys.exit("\nLine %d '%s' does not have a Shrimp format" % (self.currentLineNb, line))
+
+        mapping = Mapping()
+
+        mapping.queryInterval.setName(m.group(1))
+        mapping.queryInterval.setStart(min(int(m.group(6)), int(m.group(7))))
+        mapping.queryInterval.setEnd(max(int(m.group(6)), int(m.group(7))))
+
+        mapping.targetInterval.setChromosome(m.group(2))
+        mapping.targetInterval.setStart(min(int(m.group(4)), int(m.group(5))))
+        mapping.targetInterval.setEnd(max(int(m.group(4)), int(m.group(5))))
+
+        mapping.setSize(int(m.group(8)))
+        mapping.setDirection(m.group(3))
+
+        editString = m.group(10)
+        nbMismatches = 0
+        nbGaps = 0
+        while editString != "":
+            m = re.search(r"^(\d+)(\D.*)$", editString)
+            if m != None:
+                editString = m.group(2)
+            else:
+                m = re.search(r"^(\d+)$", editString)
+                if m != None:
+                    editString = ""
+                else:
+                    m = re.search(r"^([A-Z])(.*)$", editString)
+                    if m != None:
+                        nbMismatches += 1
+                        editString = m.group(2)
+                    else:
+                        m = re.search(r"^\((\w+)\)(.*)$", editString)
+                        if m != None:
+                            nbGaps += len(m.group(1))
+                            editString = m.group(2)
+                        else:
+                            m = re.search(r"^-(.*)$", editString)
+                            if m != None:
+                                nbGaps += 1
+                                editString = m.group(1)
+                            else:
+                                sys.exit("Cannot understand edit string %s from line %s" % (editString, line))
+
+        mapping.setNbMismatches(nbMismatches)
+        mapping.setNbGaps(nbGaps)
+
+        return mapping