--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/mergeSlidingWindowsClusters.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,144 @@
+#! /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.
+#
+"""
+Merge sliding windows of two different clusterings
+"""
+
+import sys
+import re
+import os
+from optparse import OptionParser
+from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+from commons.core.writer.Gff3Writer import Gff3Writer
+from SMART.Java.Python.misc.Progress import Progress
+from SMART.Java.Python.structure.Transcript import Transcript
+
+class MergeSlidingWindowsClusters(object):
+    """
+    Merge the ouptput of several sets of sliding windows
+    """
+
+    def __init__(self, verbosity = 0):
+        self.verbosity     = verbosity
+        self.inputs        = []
+        self.outputData    = {}
+        self.nbData        = 0
+        self.nbWrittenData = 0
+        self.chromosomes   = []
+        self.writer        = None
+
+    def __del__(self):
+        if self.writer != None:
+            self.writer.close()
+
+    def addInput(self, fileName, fileFormat):
+        self.inputs.append(TranscriptContainer(fileName, fileFormat, self.verbosity))
+        self.chromosomes = list(set(self.chromosomes).union(set(self.inputs[-1].getChromosomes())))
+
+    def setOutput(self, fileName):
+        self.writer = Gff3Writer(fileName, self.verbosity)
+
+    def readInput(self, i, chromosome):
+        progress = Progress(self.inputs[i].getNbTranscripts(), "Reading file #%d -- chromosome %s" % (i+1, chromosome), self.verbosity)
+        for transcript in self.inputs[i].getIterator():
+            progress.inc()
+            if chromosome != transcript.getChromosome(): continue
+            start     = transcript.getStart()
+            end       = transcript.getEnd()
+            direction = transcript.getDirection()
+            tags      = transcript.tags
+            if chromosome not in self.outputData:
+                self.outputData[chromosome] = {}
+            if direction not in self.outputData[chromosome]:
+                self.outputData[chromosome][direction] = {}
+            if start not in self.outputData[chromosome][direction]:
+                self.outputData[chromosome][direction][start] = {}
+            if end in self.outputData[chromosome][direction][start]:
+                ends = self.outputData[chromosome][direction][start].keys()
+                if ends[0] != end:
+                    sys.exit("Error! Two regions starting at %d end are not consistent (%d and %d) in %s on strand %d" % (start, end, ends[0], chromosome, direction))
+                self.outputData[chromosome][direction][start][end].update(tags)
+            else:
+                self.outputData[chromosome][direction][start][end] = tags
+                self.nbData += 1
+        progress.done()
+
+
+    def writeOutput(self, chromosome):
+        progress = Progress(self.nbData - self.nbWrittenData, "Writing output for chromosome %s" % (chromosome), self.verbosity)
+        for direction in self.outputData[chromosome]:
+            for start in self.outputData[chromosome][direction]:
+                for end in self.outputData[chromosome][direction][start]:
+                    transcript = Transcript()
+                    transcript.setChromosome(chromosome)
+                    transcript.setStart(start)
+                    transcript.setEnd(end)
+                    transcript.setDirection(direction)
+                    transcript.tags = self.outputData[chromosome][direction][start][end]
+                    transcript.setName("region_%d" % (self.nbWrittenData + 1))
+                    tags = transcript.getTagNames()
+                    for tag in tags:
+                        if tag.startswith("Name_") or tag.startswith("ID_"):
+                            del transcript.tags[tag]
+                    self.nbWrittenData += 1
+                    self.writer.addTranscript(transcript)
+                    progress.inc()
+        self.writer.write()
+        progress.done()
+        self.outputData = {}
+
+    def merge(self):
+        for chromosome in self.chromosomes:
+            for i, input in enumerate(self.inputs):
+                self.readInput(i, chromosome)
+            self.writeOutput(chromosome)
+        self.writer.close()
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Merge Sliding Windows Clusters v1.0.2: Merge two files containing the results of a sliding windows clustering. [Category: Sliding Windows]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input1",       dest="inputFileName1", action="store",                     type="string", help="input file 1 [compulsory] [format: file in transcript format given by -f]")
+    parser.add_option("-f", "--inputFormat1", dest="inputFormat1",   action="store",                     type="string", help="format of the input file 1 [compulsory] [format: transcript file format]")
+    parser.add_option("-j", "--input2",       dest="inputFileName2", action="store",                     type="string", help="input file 2 [compulsory] [format: file in transcript format given by -g]")
+    parser.add_option("-g", "--inputFormat2", dest="inputFormat2",   action="store",                     type="string", help="format of the input file 2 [compulsory] [format: transcript 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("-v", "--verbosity",    dest="verbosity",      action="store",      default=1,     type="int",    help="trace level [format: int]")
+    (options, args) = parser.parse_args()
+
+    merger = MergeSlidingWindowsClusters(options.verbosity)
+    merger.addInput(options.inputFileName1, options.inputFormat1)
+    merger.addInput(options.inputFileName2, options.inputFormat2)
+    merger.setOutput(options.outputFileName)
+    merger.merge()