--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/getInfoPerCoverage.py	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,167 @@
+#! /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 a transcript list and list of read, and get some info depending on the coverage"""
+
+import os
+from optparse import OptionParser
+from commons.core.parsing.SequenceListParser import *
+from commons.core.writer.Gff3Writer import *
+from SMART.Java.Python.mySql.MySqlConnection import *
+from SMART.Java.Python.structure.TranscriptListsComparator import *
+from SMART.Java.Python.misc.RPlotter import *
+from SMART.Java.Python.misc.Progress import *
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Get Info per Coverage v1.0.1: Get a list of information clustered by the density of the coverage on a genome. [Category: Personnal]"
+
+    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 TXT format]")
+    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",            default=None,    type="string", help="write a log file [format: bool] [default: false]")
+    (options, args) = parser.parse_args()
+
+    logHandle = None
+    if options.log != None:
+        logHandle = open(options.log, "w")
+        
+    transcriptContainer1 = TranscriptContainer(options.inputFileName1, options.format1, options.verbosity)
+    transcriptContainer2 = TranscriptContainer(options.inputFileName2, options.format2, options.verbosity)
+    
+    transcriptListComparator = TranscriptListsComparator(logHandle, options.verbosity)
+    transcriptListComparator.restrictToStart(transcriptListComparator.REFERENCE, 10)
+    transcriptListComparator.getColinearOnly(True)
+    transcriptListComparator.computeOddsPerTranscript(True)
+    transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.QUERY, transcriptContainer1)
+    transcriptListComparator.setInputTranscriptContainer(transcriptListComparator.REFERENCE, transcriptContainer2)
+    transcriptListComparator.compareTranscriptList()
+    transcriptTables = transcriptListComparator.getOutputTables()
+    
+    sizesWithIntrons                     = {}
+    sizesWithoutIntrons                = {}
+    nbExons                                        = {}
+    averageSizesWithIntrons        = {}
+    averageSizesWithoutIntrons = {}
+    averageNbExons                         = {}
+    sumSizesWithIntrons                = {}
+    sumSizesWithoutIntrons         = {}
+    sumSizesNbExons                        = {}
+    coverages                                    = transcriptListComparator.getOddsPerTranscript()
+
+    progress = Progress(transcriptContainer2.getNbTranscripts(), "Reading transcript file again", options.verbosity)
+    for transcript in transcriptContainer2.getIterator():
+        if transcript.name in coverages:
+            if transcript.getSizeWithIntrons() not in averageSizesWithIntrons:
+                averageSizesWithIntrons[transcript.getSizeWithIntrons()] = coverages[transcript.name]
+            else:
+                averageSizesWithIntrons[transcript.getSizeWithIntrons()] += coverages[transcript.name]
+            if transcript.getSizeWithIntrons() not in sumSizesWithIntrons:
+                sumSizesWithIntrons[transcript.getSizeWithIntrons()] = 1
+            else:
+                sumSizesWithIntrons[transcript.getSizeWithIntrons()] += 1
+            if transcript.getSize() not in averageSizesWithoutIntrons:
+                averageSizesWithoutIntrons[transcript.getSize()] = coverages[transcript.name]
+            else:
+                averageSizesWithoutIntrons[transcript.getSize()] += coverages[transcript.name]
+            if transcript.getSize() not in sumSizesWithoutIntrons:
+                sumSizesWithoutIntrons[transcript.getSize()] = 1
+            else:
+                sumSizesWithoutIntrons[transcript.getSize()] += 1
+            if transcript.getNbExons() not in averageNbExons:
+                averageNbExons[transcript.getNbExons()] = coverages[transcript.name]
+            else:
+                averageNbExons[transcript.getNbExons()] += coverages[transcript.name]
+            if transcript.getNbExons() not in sumSizesNbExons:
+                sumSizesNbExons[transcript.getNbExons()] = 1
+            else:
+                sumSizesNbExons[transcript.getNbExons()] += 1
+            sizesWithIntrons[transcript.name]        = (transcript.getSizeWithIntrons(), coverages[transcript.name])
+            sizesWithoutIntrons[transcript.name] = (transcript.getSize(), coverages[transcript.name])
+            nbExons[transcript.name]                         = (transcript.getNbExons(), coverages[transcript.name])
+        progress.inc()
+    progress.done()
+        
+    plotterSizeWithIntrons = RPlotter("%sWithIntrons.png" % (options.output), options.verbosity)
+    plotterSizeWithIntrons.setPoints(True)
+    plotterSizeWithIntrons.setMaximumX(10000)
+    plotterSizeWithIntrons.setMaximumY(1000)    
+    plotterSizeWithIntrons.setLog("y")
+    plotterSizeWithIntrons.addLine(sizesWithIntrons)
+    plotterSizeWithIntrons.plot()
+    
+    plotterSizeWithoutIntrons = RPlotter("%sWithoutIntrons.png" % (options.output), options.verbosity)
+    plotterSizeWithoutIntrons.setPoints(True)
+    plotterSizeWithoutIntrons.setMaximumX(10000)    
+    plotterSizeWithoutIntrons.setMaximumY(1000)
+    plotterSizeWithoutIntrons.setLog("y")
+    plotterSizeWithoutIntrons.addLine(sizesWithoutIntrons)
+    plotterSizeWithoutIntrons.plot()
+    
+    plotterNbExons = RPlotter("%sNbExons.png" % (options.output), options.verbosity)
+    plotterNbExons.setPoints(True)
+    plotterNbExons.addLine(nbExons)
+    plotterNbExons.plot()
+    
+    for element in averageSizesWithIntrons:
+        averageSizesWithIntrons[element] = int(float(averageSizesWithIntrons[element]) / sumSizesWithIntrons[element])
+    plotterAverageSizeWithIntrons = RPlotter("%sAverageWithIntrons.png" % (options.output), options.verbosity)
+    plotterAverageSizeWithIntrons.setMaximumX(10000)
+    plotterAverageSizeWithIntrons.setMaximumY(1000)    
+    plotterAverageSizeWithIntrons.setLog("y")
+    plotterAverageSizeWithIntrons.addLine(averageSizesWithIntrons)
+    plotterAverageSizeWithIntrons.plot()
+    print "min/avg/med/max sizes with introns: %d/%.2f/%.1f/%d" % Utils.getMinAvgMedMax(averageSizesWithIntrons)
+
+    for element in averageSizesWithoutIntrons:
+        averageSizesWithoutIntrons[element] = int(float(averageSizesWithoutIntrons[element]) / sumSizesWithoutIntrons[element])
+    plotterAverageSizeWithoutIntrons = RPlotter("%sAverageWithoutIntrons.png" % (options.output), options.verbosity)
+    plotterAverageSizeWithoutIntrons.setMaximumX(10000)
+    plotterAverageSizeWithoutIntrons.setMaximumY(1000)    
+    plotterAverageSizeWithoutIntrons.setLog("y")
+    plotterAverageSizeWithoutIntrons.addLine(averageSizesWithoutIntrons)
+    plotterAverageSizeWithoutIntrons.plot()
+    print "min/avg/med/max sizes without introns: %d/%.2f/%.1f/%d" % Utils.getMinAvgMedMax(averageSizesWithoutIntrons)
+
+    for element in averageNbExons:
+        averageNbExons[element] = int(float(averageNbExons[element]) / sumSizesNbExons[element])
+    plotterAverageNbExons = RPlotter("%sAverageNbExons.png" % (options.output), options.verbosity)
+    plotterAverageNbExons.addLine(averageNbExons)
+    plotterAverageNbExons.plot()
+    print "min/avg/med/max # exons: %d/%.2f/%.1f/%d" % Utils.getMinAvgMedMax(averageNbExons)
+
+    if options.log:
+        logHandle.close()