--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/plotRepartition.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,128 @@
+#! /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.
+#
+"""
+Plot the data from the data files
+"""
+import os
+from optparse import OptionParser
+from commons.core.parsing.GffParser import GffParser
+from SMART.Java.Python.misc.RPlotter import RPlotter
+from SMART.Java.Python.misc.Progress import Progress
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Plot Repartition v1.0.1: Plot the repartition of different data on a whole genome. (This tool uses 1 input file only, the different values being stored in the tags.    See documentation to know more about it.) [Category: Visualization]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input",     dest="inputFileName",  action="store",                           type="string", help="input file name [compulsory] [format: file in GFF3 format]")
+    parser.add_option("-n", "--names",     dest="names",          action="store",      default=None,        type="string", help="name for the tags (separated by commas and no space) [default: None] [format: string]")
+    parser.add_option("-o", "--output",    dest="outputFileName", action="store",                           type="string", help="output file [compulsory] [format: output file in PNG format]")
+    parser.add_option("-c", "--color",     dest="colors",         action="store",      default=None,        type="string", help="color of the lines (separated by commas and no space) [format: string]")
+    parser.add_option("-f", "--format",    dest="format",         action="store",      default="png",       type="string", help="format of the output file [format: string] [default: png]")
+    parser.add_option("-r", "--normalize", dest="normalize",      action="store_true", default=False,                      help="normalize data (when panels are different) [format: bool] [default: false]")
+    parser.add_option("-l", "--log",       dest="log",            action="store",      default="",          type="string", help="use log on x- or y-axis (write 'x', 'y' or 'xy') [format: string]")
+    parser.add_option("-v", "--verbosity", dest="verbosity",      action="store",      default=1,           type="int",    help="trace level [format: int]")
+    parser.add_option("-D", "--directory", dest="working_Dir",    action="store",      default=os.getcwd(), type="string", help="the directory to store the results [format: directory]")
+    (options, args) = parser.parse_args()
+
+    strands        = [1, -1]
+    strandToString = {1: "+", -1: "-"}
+    names          = [None] if options.names == None else options.names.split(",")
+    maxs           = {}
+    nbElements     = [0 for name in names]
+    lines          = [{} for i in range(len(names))]
+    if options.colors == None:
+        colors = [None for i in range(len(names))]
+    else:
+        colors = options.colors.split(",")
+
+    parser = GffParser(options.inputFileName, options.verbosity)
+    progress = Progress(parser.getNbTranscripts(), "Reading %s" % (options.inputFileName), options.verbosity)
+    for transcript in parser.getIterator():
+        chromosome = transcript.getChromosome()
+        direction  = transcript.getDirection()
+        start      = transcript.getStart()
+        for i, name in enumerate(names):
+            if chromosome not in lines[i]:
+                lines[i][chromosome] = dict([(strand, {}) for strand in strands])
+            if chromosome not in maxs:
+                maxs[chromosome] = transcript.getStart()
+            else:
+                maxs[chromosome] = max(maxs[chromosome], start)
+            if start not in lines[i][chromosome][direction]:
+                lines[i][chromosome][direction][start] = 0
+            thisNbElements                          = float(transcript.getTagValue(name)) if name != None and name in transcript.getTagNames() else 1
+            lines[i][chromosome][direction][start] += thisNbElements * direction
+            nbElements[i]                          += thisNbElements
+        progress.inc()
+    progress.done()
+
+    if options.normalize:
+        if options.verbosity >= 10:
+            print "Normalizing..."
+        for i, linesPerCondition in enumerate(lines):
+            for linesPerChromosome in linesPerCondition.values():
+                for line in linesPerChromosome.values():
+                    for key, value in line.iteritems():
+                        line[key] = value / float(nbElements[i]) * max(nbElements)
+    if options.verbosity >= 10:
+        print "... done."
+
+    progress = Progress(len(maxs.keys()), "Plotting", options.verbosity)
+    for chromosome in maxs:
+        plot = RPlotter("%s%s.%s" % (options.outputFileName, chromosome.capitalize(), options.format), options.verbosity)
+        plot.setLog(options.log)
+        plot.setImageSize(2000, 500)
+        plot.setFormat(options.format)
+        if maxs[chromosome] <= 1000:
+            unit    = "nt."
+            ratio = 1.0
+        elif maxs[chromosome] <= 1000000:
+            unit    = "kb"
+            ratio = 1000.0
+        else:
+            unit    = "Mb"
+            ratio = 1000000.0
+        plot.setXLabel("Position on %s (in %s)" % (chromosome.replace("_", " "), unit))
+        plot.setYLabel("# reads")
+        plot.setLegend(True)
+        for i, name in enumerate(names):
+            for strand in strands:
+                correctedLine = dict([(key / ratio, value) for key, value in lines[i][chromosome][strand].iteritems()])
+                if name != None:
+                    name = "%s (%s)" % (name.replace("_", " "), strandToString[strand])
+                plot.addLine(correctedLine, None, colors[i])
+        plot.plot()
+        progress.inc()
+    progress.done()
+