--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/Soap2Parser.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,148 @@
+#
+# 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 SMART.Java.Python.structure.SubMapping import SubMapping
+from commons.core.parsing.MapperParser import MapperParser
+
+
+def mappingToSubMapping(mapping):
+    subMapping = SubMapping()
+    subMapping.targetInterval.copy(mapping.targetInterval)
+    subMapping.queryInterval.copy(mapping.queryInterval)
+    subMapping.setDirection(mapping.getDirection())
+    subMapping.size = mapping.size
+    subMapping.tags = mapping.tags
+    return subMapping
+
+
+
+class Soap2Parser(MapperParser):
+    """A class that parses the output of SOAP2"""
+
+    def __init__(self, fileName, verbosity = 0):
+        super(Soap2Parser, self).__init__(fileName, verbosity)
+
+
+    def __del__(self):
+        super(Soap2Parser, self).__del__()
+
+
+    def getFileFormats():
+        return ["soap2"]
+    getFileFormats = staticmethod(getFileFormats)
+
+
+    def skipFirstLines(self):
+        pass
+
+
+    def getIterator(self):
+        self.reset()
+        currentName = None
+        currentMappings = []
+        for line in self.handle:
+            mapping = self.parseLine(line)
+            name = mapping.queryInterval.name
+            if name == currentName:
+                if mapping.getTagValue("end") == "a":
+                    currentMappings.append(mapping)
+                else:
+                    otherEndMapping = currentMappings.pop(0)
+
+                    newMapping = Mapping()
+                    subMappingA = mappingToSubMapping(otherEndMapping)
+                    subMappingB = mappingToSubMapping(mapping)
+                    subMappingB.queryInterval.setDirection(subMappingA.queryInterval.getDirection())
+
+                    newMapping.addSubMapping(subMappingA)
+                    newMapping.addSubMapping(subMappingB)
+
+                    newMapping.tags = otherEndMapping.tags
+                    newMapping.setSize(otherEndMapping.size + mapping.size)
+                    newMapping.setNbMismatches(otherEndMapping.getTagValue("nbMismatches") + mapping.getTagValue("nbMismatches"))
+                    print otherEndMapping.getTagValue("nbMismatches")
+                    print mapping.getTagValue("nbMismatches")
+                    print newMapping.getTagValue("nbMismatches")
+                    sys.exit()
+                    newMapping.setTagValue("qualityString", otherEndMapping.getTagValue("qualityString") + mapping.getTagValue("qualityString"))
+                    newMapping.setTagValue("occurrence", "%d" % (newMapping.getTagValue("nbOccurrences") - len(currentMappings)))
+                    newMapping.setTagValue("ID", "%s-%s" % (name, newMapping.getTagValue("occurrence")))
+                    del newMapping.tags["end"]
+                    yield newMapping
+            else:
+                currentName = mapping.queryInterval.name
+                for currentMapping in currentMappings:
+                    yield currentMapping
+                currentMappings = [mapping]
+            self.currentLineNb += 1
+                
+                
+    def parseLine(self, line):
+        m = re.search(r"^\s*(\S+)\s+(\w+)\s+(\S+)\s+(\d+)\s+([ab])\s+(\d+)\s+([+-])\s+(\w+)\s+(\d+)\s+(\d+)\s+", line)
+        if m == None:
+            sys.exit("\nLine %d '%s' does not have a SOAP2 format" % (self.currentLineNb, line))
+
+        name          = m.group(1)
+        read          = m.group(2)
+        qualityString = m.group(3)
+        nbOccurrences = int(m.group(4))
+        end           = m.group(5)
+        size          = int(m.group(6))
+        direction     = m.group(7)
+        chromosome    = m.group(8)
+        genomeStart   = int(m.group(9))
+        nbMismatches  = int(m.group(10))
+
+        mapping = Mapping()
+        if name.endswith("/1") or name.endswith("/2"):
+            name = name[:-2]
+
+        mapping.queryInterval.name = name
+        mapping.queryInterval.setDirection(direction)
+        mapping.queryInterval.setStart(1)
+        mapping.queryInterval.setEnd(size)
+
+        mapping.targetInterval.setChromosome(chromosome)
+        mapping.targetInterval.setStart(genomeStart)
+        mapping.targetInterval.setSize(size)
+
+        mapping.setDirection(direction)
+        mapping.setSize(size)
+
+        mapping.setNbMismatches(nbMismatches)
+        mapping.setNbGaps(0)
+        mapping.setTagValue("qualityString", qualityString)
+        mapping.setTagValue("nbOccurrences", nbOccurrences)
+        mapping.setTagValue("end", end)
+
+        return mapping
+