--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/getReadDistribution.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,129 @@
+#! /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.FastaParser import FastaParser
+from commons.core.parsing.FastqParser import FastqParser
+from SMART.Java.Python.misc.RPlotter import RPlotter
+from SMART.Java.Python.misc.Progress import Progress
+from SMART.Java.Python.misc import Utils
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Get Read Distribution v1.0.1: Plot the number of identical reads and give the most represented. [Category: Visualization]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input",     dest="inputFileName",  action="store",               type="string", help="input file sequence [compulsory] [format: file in sequence format given by -f]")
+    parser.add_option("-f", "--format",    dest="format",         action="store",               type="string", help="format of the file [compulsory] [format: sequence file format]")
+    parser.add_option("-n", "--number",    dest="number",         action="store", default=None, type="int",    help="keep the best n    [format: int]")
+    parser.add_option("-p", "--percent",   dest="percent",        action="store", default=None, type="float",  help="keep the best n\% [format: float]")
+    parser.add_option("-o", "--output",    dest="outputFileName", action="store",               type="string", help="output file [compulsory] [format: output files in PNG format and txt format]")
+    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("-D", "--directory", dest="working_Dir",    action="store", default=os.getcwd(), type="string", help="the directory to store the results [format: directory]")
+    parser.add_option("-v", "--verbosity", dest="verbosity",      action="store", default=1,    type="int",    help="trace level [format: int]")
+    (options, args) = parser.parse_args()
+
+    if options.working_Dir[-1] != '/':
+        options.outputFileName = options.working_Dir + '/' + options.outputFileName
+        
+    if options.format == "fasta":
+        parser = FastaParser(options.inputFileName, options.verbosity)
+    elif options.format == "fastq":
+        parser = FastqParser(options.inputFileName, options.verbosity)
+    else:
+        raise Exception("Do not understand '%s' file format." % (options.format))
+
+    progress  = Progress(parser.getNbSequences(), "Reading %s" % (options.inputFileName), options.verbosity)
+    sequences = {}
+    for sequence in parser.getIterator():
+        sequence = sequence.sequence
+        if sequence not in sequences:
+            sequences[sequence] = 1
+        else:
+            sequences[sequence] += 1
+        progress.inc()
+    progress.done()
+
+    values = sequences.values()
+    values.sort()
+    if options.percent != None:
+        threshold = values[int(float(options.percent) / 100 * len(values))]
+    elif options.number != None:
+        threshold = values[-options.number]
+    else:
+        threshold = 0
+
+    # sort by value
+    progress     = Progress(parser.getNbSequences(), "Sorting values", options.verbosity)
+    sortedValues = dict([(value, []) for value in sequences.values()])
+    for sequence, value in sequences.iteritems():
+        sortedValues[value].append(sequence)
+        progress.inc()
+    progress.done()
+
+    outputFileName = "%s.txt" % (options.outputFileName)
+    handle         = open(outputFileName, "w")
+    progress       = Progress(parser.getNbSequences(), "Writing into %s" % (outputFileName), options.verbosity)
+    for value in reversed(sorted(sortedValues.keys())):
+        if value >= threshold:
+            for sequence in sortedValues[value]:
+                handle.write("%s\t%d\n" % (sequence, value))
+        progress.inc()
+    progress.done()
+    handle.close()
+
+    line     = {}
+    progress = Progress(len(values), "Preparing plot", options.verbosity)
+    for value in values:
+        if value not in line:
+            line[value] = 1
+        else:
+            line[value] += 1
+        progress.inc()
+    progress.done()
+
+    plot = RPlotter("%s.png" % (options.outputFileName), options.verbosity)
+    plot.setFill(0)
+    plot.setMaximumX(options.xMax)
+    plot.setXLabel("# occurrences")
+    plot.setYLabel("# reads")
+    plot.addLine(line)
+    plot.plot()
+
+    if options.verbosity > 0:
+        print "%d/%.2f/%.1f/%d occurrences" % (Utils.getMinAvgMedMax(line))
+
+