--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/compareOverlapping.py	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,126 @@
+#! /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.
+#
+"""Compare overlap of two transcript lists"""
+import sys
+import os
+from optparse import OptionParser
+from SMART.Java.Python.misc import Utils
+from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+from commons.core.writer.TranscriptWriter import TranscriptWriter
+from SMART.Java.Python.structure.TranscriptListsComparator import TranscriptListsComparator
+from SMART.Java.Python.misc.RPlotter import RPlotter
+from commons.core.writer.Gff3Writer import Gff3Writer
+
+class CompareOverlapping(object):
+
+    def __init__(self):
+        self._options = None
+
+
+    def setAttributesFromCmdLine(self):
+        description = "Compare Overlapping v1.0.3: Get the data which overlap with a reference set. [Category: Data Comparison]"
+
+        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", "--format1",          dest="format1",        action="store",                     type="string", help="format of 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", "--format2",          dest="format2",        action="store",                     type="string", help="format of file 2 [compulsory] [format: transcript file format]")
+        parser.add_option("-o", "--output",           dest="output",         action="store",      default=None,  type="string", help="output file [compulsory] [format: output file in GFF3 format]")
+        parser.add_option("-S", "--start1",           dest="start1",         action="store",      default=None,  type="int",    help="only consider the n first nucleotides of the transcripts in file 1 (do not use it with -U) [format: int]")
+        parser.add_option("-s", "--start2",           dest="start2",         action="store",      default=None,  type="int",    help="only consider the n first nucleotides of the transcripts in file 2 (do not use it with -u) [format: int]")
+        parser.add_option("-U", "--end1",             dest="end1",           action="store",      default=None,  type="int",    help="only consider the n last nucleotides of the transcripts in file 1 (do not use it with -S) [format: int]")
+        parser.add_option("-u", "--end2",             dest="end2",           action="store",      default=None,  type="int",    help="only consider the n last nucleotides of the transcripts in file 2 (do not use it with -s) [format: int]")
+        parser.add_option("-t", "--intron",           dest="introns",        action="store_true", default=False,                help="also report introns [format: bool] [default: false]")
+        parser.add_option("-E", "--5primeExtension1", dest="fivePrime1",     action="store",      default=None,  type="int",    help="extension towards 5' in file 1 [format: int]")
+        parser.add_option("-e", "--5primeExtension2", dest="fivePrime2",     action="store",      default=None,  type="int",    help="extension towards 5' in file 2 [format: int]")
+        parser.add_option("-N", "--3primeExtension1", dest="threePrime1",    action="store",      default=None,  type="int",    help="extension towards 3' in file 1 [format: int]")
+        parser.add_option("-n", "--3primeExtension2", dest="threePrime2",    action="store",      default=None,  type="int",    help="extension towards 3' in file 2 [format: int]")
+        parser.add_option("-c", "--colinear",         dest="colinear",       action="store_true", default=False,                help="colinear only [format: bool] [default: false]")
+        parser.add_option("-a", "--antisense",        dest="antisense",      action="store_true", default=False,                help="antisense only [format: bool] [default: false]")
+        parser.add_option("-d", "--distance",         dest="distance",       action="store",      default=None,  type="int",    help="accept some distance between query and reference [format: int]")
+        parser.add_option("-k", "--included",         dest="included",       action="store_true", default=False,                help="keep only elements from file 1 which are included in an element of file 2 [format: bool] [default: false]")
+        parser.add_option("-K", "--including",        dest="including",      action="store_true", default=False,                help="keep only elements from file 2 which are included in an element of file 1 [format: bool] [default: false]")
+        parser.add_option("-m", "--minOverlap",       dest="minOverlap",     action="store",      default=1,     type="int",    help="minimum number of nucleotides overlapping to declare an overlap [format: int] [default: 1]")
+        parser.add_option("-p", "--pcOverlap",        dest="pcOverlap",      action="store",      default=None,  type="int",    help="minimum percentage of nucleotides to overlap to declare an overlap [format: int]")
+        parser.add_option("-O", "--notOverlapping",   dest="notOverlapping", action="store_true", default=False,                help="also output not overlapping data [format: bool] [default: false]")
+        parser.add_option("-x", "--exclude",          dest="exclude",        action="store_true", default=False,                help="invert the match [format: bool] [default: false]")
+        parser.add_option("-v", "--verbosity",        dest="verbosity",      action="store",      default=1,     type="int",    help="trace level [format: int]")
+        parser.add_option("-l", "--log",              dest="log",            action="store_true", default=False,                help="write a log file [format: bool] [default: false]")
+        (self._options, args) = parser.parse_args()
+
+
+    def run(self):             
+        logHandle = None
+        if self._options.log:
+            logHandle = open(self._options.output, "w")
+
+        transcriptContainer1 = TranscriptContainer(self._options.inputFileName1, self._options.format1, self._options.verbosity)
+        transcriptContainer2 = TranscriptContainer(self._options.inputFileName2, self._options.format2, self._options.verbosity)
+        writer               = TranscriptWriter(self._options.output, "gff3", self._options.verbosity)
+
+        transcriptListComparator = TranscriptListsComparator(logHandle, self._options.verbosity)
+        transcriptListComparator.restrictToStart(transcriptListComparator.QUERY, self._options.start1)
+        transcriptListComparator.restrictToStart(transcriptListComparator.REFERENCE, self._options.start2)
+        transcriptListComparator.restrictToEnd(transcriptListComparator.QUERY, self._options.end1)
+        transcriptListComparator.restrictToEnd(transcriptListComparator.REFERENCE, self._options.end2)
+        transcriptListComparator.extendFivePrime(transcriptListComparator.QUERY, self._options.fivePrime1)
+        transcriptListComparator.extendFivePrime(transcriptListComparator.REFERENCE, self._options.fivePrime2)
+        transcriptListComparator.extendThreePrime(transcriptListComparator.QUERY, self._options.threePrime1)
+        transcriptListComparator.extendThreePrime(transcriptListComparator.REFERENCE, self._options.threePrime2)
+        transcriptListComparator.acceptIntrons(transcriptListComparator.QUERY, self._options.introns)
+        transcriptListComparator.acceptIntrons(transcriptListComparator.REFERENCE, self._options.introns)
+        transcriptListComparator.getAntisenseOnly(self._options.antisense)
+        transcriptListComparator.getColinearOnly(self._options.colinear)
+        transcriptListComparator.getInvert(self._options.exclude)
+        transcriptListComparator.setMaxDistance(self._options.distance)
+        transcriptListComparator.setMinOverlap(self._options.minOverlap)
+        transcriptListComparator.setPcOverlap(self._options.pcOverlap)
+        transcriptListComparator.setIncludedOnly(self._options.included)
+        transcriptListComparator.setIncludingOnly(self._options.including)
+        transcriptListComparator.includeNotOverlapping(self._options.notOverlapping)
+        transcriptListComparator.computeOdds(True)
+        transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.QUERY, transcriptContainer1)
+        transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.REFERENCE, transcriptContainer2)
+        transcriptListComparator.setOutputWriter(writer)
+        transcriptListComparator.compareTranscriptList()
+
+        if self._options.log:
+            logHandle.close()
+
+        if not self._options.exclude:
+            odds = transcriptListComparator.getOdds()
+            if self._options.verbosity > 0 and odds:
+                print "min/avg/med/max transcripts: %d/%.2f/%.1f/%d" % Utils.getMinAvgMedMax(odds)
+                
+if __name__ == "__main__":
+    icompareOverlapping = CompareOverlapping()
+    icompareOverlapping.setAttributesFromCmdLine()
+    icompareOverlapping.run()