--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/commons/core/parsing/PslParser.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,155 @@
+#
+# 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 commons.core.parsing.MapperParser import MapperParser
+from SMART.Java.Python.structure.Mapping import Mapping
+from SMART.Java.Python.structure.SubMapping import SubMapping
+from SMART.Java.Python.structure.Interval import Interval
+from SMART.Java.Python.misc.UnlimitedProgress import UnlimitedProgress
+
+class PslParser(MapperParser):
+    """A class that parses the output of PSL format (of SSAHA and BLAT)"""
+
+    def __init__(self, fileName, verbosity = 0):
+        super(PslParser, self).__init__(fileName, verbosity)
+
+
+    def __del__(self):
+        super(PslParser, self).__del__()
+
+
+    def getFileFormats():
+        return ["psl"]
+    getFileFormats = staticmethod(getFileFormats)
+
+
+    def getInfos(self):
+        self.chromosomes = set()
+        self.nbMappings  = 0
+        self.size        = 0
+        self.reset()
+        progress = UnlimitedProgress(100000, "Getting info on PSL file, # mappings read:", self.verbosity)
+        for line in self.handle:
+            progress.inc()
+            line = line.strip()
+            if line == "":
+                continue
+            parts      = line.split("\t")
+            chromosome = parts[13]
+            self.chromosomes.add(chromosome)
+            self.nbMappings += 1
+            self.size += len(parts[0])
+        self.reset()
+        progress.done()
+
+
+    def skipFirstLines(self):
+        while "------" not in self.handle.readline():
+            self.currentLineNb += 1
+            pass
+
+    def _computeStarts(self,seqSize,blockSize,start,targetStrand):
+        if targetStrand == "+":
+            pass
+        else:
+            start = seqSize-blockSize-start
+        return start
+            
+
+
+    def parseLine(self, line):
+        m = re.search(r"^\s*(psl:\s+)?(\d+)\s+(\d+)\s+(\d+)\s+\d+\s+\d+\s+(\d+)\s+\d+\s+(\d+)\s+([+-]{1,2})\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\d+)\s+(\S+)\s+(\S+)\s+(\S+)\s*$", line)
+        if m == None:
+            raise Exception("\nLine %d '%s' does not have a PSL format" % (self.currentLineNb, line))
+
+        mapping = Mapping()
+
+        queryStrand = m.group(7)[0]
+
+        if len(m.group(7)) == 1:
+            targetStrand = "+"
+        else:
+            targetStrand = m.group(7)[1]
+
+
+        for i in range(0, int(m.group(16))):
+            size        = int(m.group(17).split(",")[i])
+            queryStart  = int(m.group(18).split(",")[i])
+            targetStart = int(m.group(19).split(",")[i])
+            querySize   = int(m.group(9))
+            targetSize  = int(m.group(13))
+            
+            subMapping = SubMapping()
+            subMapping.setSize(size)
+            subMapping.setDirection(m.group(7)[0])
+
+            queryInterval  = Interval()
+            targetInterval = Interval()
+
+            queryInterval.setName(m.group(8))
+            queryStart = self._computeStarts(querySize,size,queryStart,targetStrand)
+            queryInterval.setStart(queryStart + 1)
+            queryInterval.setEnd(queryStart + size)
+            queryInterval.setDirection(queryStrand)
+
+            targetInterval.setChromosome(m.group(12))
+            targetStart = self._computeStarts(targetSize,size,targetStart,targetStrand)
+            targetInterval.setStart(targetStart + 1)
+            targetInterval.setEnd(targetStart + size)
+            targetInterval.setDirection(targetStrand)
+
+            subMapping.setQueryInterval(queryInterval)
+            subMapping.setTargetInterval(targetInterval)
+            mapping.addSubMapping(subMapping)
+
+        mapping.setSize(int(m.group(2)) + int(m.group(3)) + int(m.group(4)))
+        mapping.setNbMismatches(int(m.group(3)) + int(m.group(4)))
+        mapping.setNbGaps(int(m.group(5)))
+        mapping.setDirection(queryStrand)
+
+        queryInterval  = Interval()
+        targetInterval = Interval()
+
+        queryInterval.setName(m.group(8))
+        queryInterval.setStart(min(int(m.group(10)), int(m.group(11))))
+        queryInterval.setEnd(  max(int(m.group(10)), int(m.group(11))))
+        queryInterval.setDirection(queryStrand)
+
+        targetInterval.setChromosome(m.group(12))
+        targetInterval.setStart(min(int(m.group(14))+1, int(m.group(15))))
+        targetInterval.setEnd(  max(int(m.group(14))+1, int(m.group(15))))
+        targetInterval.setDirection(targetStrand)
+
+        mapping.setQueryInterval(queryInterval)
+        mapping.setTargetInterval(targetInterval)
+
+        return mapping
+