--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/AxtParser.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,154 @@
+#
+# 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
+from SMART.Java.Python.misc import Utils
+from SMART.Java.Python.misc.Utils import getHammingDistance
+
+
+class AxtParser(MapperParser):
+    """A class that parses AXT (as given by Mosaik)"""
+
+    def __init__(self, fileName, verbosity = 0):
+        super(AxtParser, self).__init__(fileName, verbosity)
+        self.queryLine = None
+        self.subjectLine = None
+
+    def __del__(self):
+        super(AxtParser, self).__del__()
+
+
+    def getFileFormats():
+        return ["axt"]
+    getFileFormats = staticmethod(getFileFormats)
+
+
+    def skipFirstLines(self):
+        pass
+
+
+    def getInfos(self):
+        self.chromosomes = set()
+        self.nbMappings  = 0
+        self.size        = 0
+        cpt              = 0
+        self.reset()
+        for line in self.handle:
+            line = line.strip()
+            if line == "": continue
+            if cpt % 3 == 0:
+                line    = line.strip()
+                parts = line.split(" ")
+                self.chromosomes.add(parts[1])
+                self.size       += int(parts[6])
+                self.nbMappings += 1
+            cpt += 1
+            if self.verbosity >= 10 and self.nbMappings % 100000 == 0:
+                sys.stdout.write("    %d mappings read\r" % (self.nbMappings))
+                sys.stdout.flush()
+        self.reset()
+        if self.verbosity >= 10:
+            print "    %d mappings read" % (self.nbMappings)
+            print "Done."
+        
+
+    def parseLine(self, line):
+
+        if line.strip() == "":
+            for line in self.handle:
+                self.currentLineNb += 1
+                break
+        if line.strip() == "":
+            return None
+
+        m = re.search(r"^\s*\d+\s+(\S+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\d+)\s+(\d+)\s+([+-])\s+\d+\s*$", line)
+        if m != None:
+            #sys.exit("\nLine %d '%s' does not have an AXT format" % (self.currentLineNb, line))
+
+            mapping = Mapping()
+            subMapping = SubMapping()
+    
+            offset = -1 if m.group(7) == "-" else 0
+            subMapping.queryInterval.setName(m.group(4))
+            subMapping.queryInterval.setStart(min(int(m.group(5)), int(m.group(6)))-1)
+            subMapping.queryInterval.setEnd(max(int(m.group(5)), int(m.group(6)))-1)
+            subMapping.queryInterval.setDirection(m.group(7))
+    
+            subMapping.targetInterval.setChromosome(m.group(1))
+            subMapping.targetInterval.setStart(min(int(m.group(2)), int(m.group(3))) + offset)
+            subMapping.targetInterval.setEnd(max(int(m.group(2)), int(m.group(3))) + offset)
+            subMapping.targetInterval.setDirection(1)
+    
+            subMapping.setSize(min(subMapping.targetInterval.getSize(), subMapping.queryInterval.getSize()))
+            subMapping.setDirection(m.group(7))
+    
+            mapping.addSubMapping(subMapping)
+    
+            mapping.setDirection(m.group(7))
+            mapping.targetInterval.setChromosome(m.group(1))
+            mapping.targetInterval.setStart(min(int(m.group(2)), int(m.group(3))) + offset)
+            mapping.targetInterval.setEnd(max(int(m.group(2)), int(m.group(3))) + offset)
+    
+            mapping.queryInterval.setName(m.group(4))
+            mapping.queryInterval.setStart(min(int(m.group(5)), int(m.group(6)))-1)
+            mapping.queryInterval.setEnd(max(int(m.group(5)), int(m.group(6)))-1)
+    
+            mapping.setSize(min(mapping.targetInterval.getSize(), mapping.queryInterval.getSize()))
+    
+            for line in self.handle:
+                string1 = line.strip()
+                self.currentLineNb += 1
+                break
+            for line in self.handle:
+                string2 = line.strip()
+                self.currentLineNb += 1
+                break
+            mapping.setNbMismatches(Utils.getHammingDistance(string1, string2))
+            mapping.setNbGaps(0)
+    
+            self.currentMapping = mapping
+        else:
+            if self.queryLine == None:
+                self.queryLine = line
+            else:
+                self.subjectLine = line
+                seqLen = float(len(self.subjectLine))
+                dist = float(getHammingDistance(self.queryLine, self.subjectLine))
+                identity = ((seqLen-dist)/seqLen) *100
+                self.currentMapping.setIdentity(identity)
+                self.queryLine = None
+                self.subjectLine = None
+                return self.currentMapping
+            
+
+