--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/CollapseReads.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,174 @@
+#! /usr/bin/env python
+#
+# 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 os
+from optparse import OptionParser, OptionGroup
+from commons.core.parsing.ParserChooser import ParserChooser
+from commons.core.writer.Gff3Writer import Gff3Writer
+from SMART.Java.Python.structure.Transcript import Transcript
+from SMART.Java.Python.ncList.NCListFilePickle import NCListFileUnpickle
+from SMART.Java.Python.ncList.FileSorter import FileSorter
+from SMART.Java.Python.misc.Progress import Progress
+
+
+class CollapseReads(object):
+    """
+    Merge two reads if they have exactly the same genomic coordinates
+    """
+
+    def __init__(self, verbosity = 0):
+        self.verbosity         = verbosity
+        self.inputReader       = None
+        self.outputWriter      = None
+        self.strands           = True
+        self.nbRead            = 0
+        self.nbWritten         = 0
+        self.nbMerges          = 0
+        self.splittedFileNames = {}
+
+    def __del__(self):
+        for fileName in self.splittedFileNames.values():
+            os.remove(fileName)
+            
+    def close(self):
+        self.outputWriter.close()
+        
+    def setInputFile(self, fileName, format):
+        parserChooser = ParserChooser(self.verbosity)
+        parserChooser.findFormat(format, "transcript")
+        self.parser = parserChooser.getParser(fileName)
+        self.sortedFileName = "%s_sorted.pkl" % (os.path.splitext(fileName)[0])
+
+    def setOutputFile(self, fileName):
+        self.outputWriter = Gff3Writer(fileName, self.verbosity)
+
+    def getNbElements(self):
+        return self.parser.getNbTranscripts()
+
+    def _sortFile(self):
+        fs = FileSorter(self.parser, self.verbosity-4)
+        fs.perChromosome(True)
+        fs.setOutputFileName(self.sortedFileName)
+        fs.sort()
+        self.splittedFileNames       = fs.getOutputFileNames()
+        self.nbElementsPerChromosome = fs.getNbElementsPerChromosome()
+        self.nbRead                  = fs.getNbElements()
+        
+    def _iterate(self, chromosome):
+        progress    = Progress(self.nbElementsPerChromosome[chromosome], "Checking chromosome %s" % (chromosome), self.verbosity)
+        transcripts = []
+        parser      = NCListFileUnpickle(self.splittedFileNames[chromosome], self.verbosity)
+        for newTranscript in parser.getIterator():
+            newTranscripts = []
+            for oldTranscript in transcripts:
+                if self._checkOverlap(newTranscript, oldTranscript):
+                    self._merge(newTranscript, oldTranscript)
+                elif self._checkPassed(newTranscript, oldTranscript):
+                    self._write(oldTranscript)
+                else:
+                    newTranscripts.append(oldTranscript)
+            newTranscripts.append(newTranscript)
+            transcripts = newTranscripts
+            progress.inc()
+        for transcript in transcripts:
+            self._write(transcript)
+        progress.done()
+
+    def _merge(self, transcript1, transcript2):
+        self.nbMerges += 1
+        transcript2.setDirection(transcript1.getDirection())
+        transcript1.merge(transcript2)
+
+    def _write(self, transcript):
+        self.nbWritten += 1
+        self.outputWriter.addTranscript(transcript)
+
+    def _checkOverlap(self, transcript1, transcript2):
+        if transcript1.getStart() != transcript2.getStart() or transcript1.getEnd() != transcript2.getEnd():
+            return False
+        return (not self.strands or transcript1.getDirection() == transcript2.getDirection())
+
+    def _checkPassed(self, transcript1, transcript2):
+        return (transcript2.getStart() < transcript1.getStart())
+
+    def collapseChromosome(self, chromosome):
+        progress            = Progress(table.getNbElements(), "Analysing chromosome %s" % (chromosome), self.verbosity)
+        command             = "SELECT * FROM %s ORDER BY start ASC, end DESC" % (table.name)
+        transcriptStart     = None
+        transcriptEnd       = None
+        transcriptDirection = None
+        currentTranscript   = None
+        if self.strands:
+            command += ", direction"
+        for index, transcript in table.selectTranscripts(command, True):
+            self.nbRead += 1
+            if not self.strands:
+                transcript.setDirection("+")
+            if transcriptStart != transcript.getStart() or transcriptEnd != transcript.getEnd() or transcriptDirection != transcript.getDirection():
+                self.writeTranscript(currentTranscript)
+                transcriptStart     = transcript.getStart()
+                transcriptEnd       = transcript.getEnd()
+                transcriptDirection = transcript.getDirection()
+                currentTranscript   = transcript
+            else:
+                currentTranscript.setTagValue("nbElements", (currentTranscript.getTagValue("nbElements") + 1) if "nbElements" in currentTranscript.getTagNames() else 1)
+            progress.inc()
+        self.writeTranscript(currentTranscript)
+        progress.done()
+
+    def collapse(self):
+        self._sortFile()
+        for chromosome in sorted(self.nbElementsPerChromosome.keys()):
+            self._iterate(chromosome)
+        self.outputWriter.close()
+        if self.verbosity > 1:
+            print "# reads read: %d" % (self.nbRead)
+            print "# reads written: %d (%.2f%%)" % (self.nbWritten, float(self.nbWritten) / self.nbRead * 100)
+            print "# reads merges: %d" % (self.nbMerges)
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Collapse Reads v1.0.3: Merge two reads if they have exactly the same genomic coordinates. [Category: Merge]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input",     dest="inputFileName",  action="store",                     type="string", help="input file [compulsory] [format: file in mapping format given by -f]")
+    parser.add_option("-f", "--format",    dest="format",         action="store",                     type="string", help="format of the file [compulsory] [format: mapping file format]")
+    parser.add_option("-o", "--output",    dest="outputFileName", action="store",                     type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+    parser.add_option("-s", "--strands",   dest="strands",        action="store_true", default=False,                help="merge elements on 2 different strands [format: bool] [default: false]")
+    parser.add_option("-v", "--verbosity", dest="verbosity",      action="store",      default=1,     type="int",    help="trace level [default: 1] [format: int]")
+    (options, args) = parser.parse_args()
+
+    collapser = CollapseReads(options.verbosity)
+    collapser.setInputFile(options.inputFileName, options.format)
+    collapser.setOutputFile(options.outputFileName)
+    collapser.strands = not options.strands
+    collapser.collapse()
+    collapser.close()