--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/getNb.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,99 @@
+#! /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.
+#
+"""Get the repartition of some elements (# exons per transcripts, # of repetitions of a mapping or # of transcripts in a cluster)"""
+
+from optparse import OptionParser
+from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+from SMART.Java.Python.misc.RPlotter import RPlotter
+from SMART.Java.Python.misc.Progress import Progress
+from SMART.Java.Python.misc import Utils
+from math import *
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Get Nb v1.0.1: Get the distribution of exons per transcripts, or mapping per read, or transcript per cluster. [Category: Visualization]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input",     dest="inputFileName",  action="store",                     type="string", help="input file [compulsory] [format: file in transcript format given by -f]")
+    parser.add_option("-f", "--format",    dest="format",         action="store",                     type="string", help="format of the input file [compulsory] [format: transcript file format]")
+    parser.add_option("-o", "--output",    dest="outputFileName", action="store",                     type="string", help="output file [compulsory] [format: output file in png format]")
+    parser.add_option("-q", "--query",     dest="query",          action="store",                     type="string", help="query  [compulsory] (# exons, # transcripts) [format: choice (exon, transcript, cluster)]")    
+    parser.add_option("-b", "--barplot",   dest="barplot",        action="store_true", default=False,                help="use barplot representation [format: bool] [default: false]")
+    parser.add_option("-x", "--xMax",      dest="xMax",           action="store",      default=None,  type="int",    help="maximum value on the x-axis to plot [format: int]")
+    parser.add_option("-v", "--verbosity", dest="verbosity",      action="store",      default=1,     type="int",    help="trace level [default: 1] [format: int]")
+    parser.add_option("-l", "--log",       dest="log",            action="store_true", default=False,                help="write a log file [format: bool] [default: false]")
+    (options, args) = parser.parse_args()
+
+    if options.query != "exon" and options.query != "transcript" and options.query != "cluster":
+        raise Exception("Do not understand query %s" % (options.query))
+
+    exonDistribution       = {}
+    transcriptDistribution = {}
+    clusterDistribution    = {}
+    
+    transcriptContainer = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
+        
+    progress = Progress(transcriptContainer.getNbTranscripts(), "Parsing %s" % (options.inputFileName), options.verbosity)
+    # count the number of reads
+    for element in transcriptContainer.getIterator():
+        if options.query == "exon":
+            nbExons = element.getNbExons()
+            exonDistribution[nbExons] = exonDistribution.get(nbExons, 0) + 1
+        elif options.query == "transcript":
+            name = element.getName()
+            transcriptDistribution[name] = transcriptDistribution.get(name, 0) + 1
+        elif options.query == "cluster":
+            nbElements = 1 if "nbElements" not in element.getTagNames() else element.getTagValue("nbElements")
+            clusterDistribution[nbElements] = clusterDistribution.get(nbElements, 0) + 1
+        progress.inc()
+    progress.done()
+    
+    if options.query == "exon":
+        distribution = exonDistribution
+    elif options.query == "transcript":
+        distribution = {}
+        for name in transcriptDistribution:
+            distribution[transcriptDistribution[name]] = distribution.get(transcriptDistribution[name], 0) + 1
+    elif options.query == "cluster":
+        distribution = clusterDistribution
+    
+    outputFileName = options.outputFileName
+    plotter = RPlotter(outputFileName, options.verbosity)
+    plotter.setImageSize(1000, 300)
+    plotter.setFill(0)
+    plotter.setMaximumX(options.xMax)
+    plotter.setBarplot(options.barplot)
+    plotter.addLine(distribution)
+    plotter.plot()
+             
+    print "min/avg/med/max: %d/%.2f/%.1f/%d" % (Utils.getMinAvgMedMax(distribution))
+