--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/selectByNbOccurrences.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,89 @@
+#! /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.
+#
+"""Select the transcript that have not more that a given number of occurrences"""
+
+import os
+from optparse import OptionParser
+from SMART.Java.Python.structure.TranscriptContainer import *
+from commons.core.writer.Gff3Writer import *
+from SMART.Java.Python.misc.Progress import *
+from SMART.Java.Python.misc.RPlotter import *
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Select by # of Occurrences v1.0.1: Keep the reads which have mapped less than a given number of times. [Category: Personnal]"
+
+    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 [compulsory] [format: transcript file format]")
+    parser.add_option("-n", "--occurrences", dest="occurrences",        action="store",            default=1,                type="int",        help="maximum number of occurrences allowed [format: int] [default: 1]")     
+    parser.add_option("-o", "--output",            dest="outputFileName", action="store",                                                type="string", help="output file [format: output file in GFF3 format]")
+    parser.add_option("-y", "--mysql",             dest="mysql",                    action="store_true", default=False,                                     help="mySQL output [format: bool] [default: false]")
+    parser.add_option("-v", "--verbosity",     dest="verbosity",            action="store",            default=1,                type="int",        help="trace level [format: int] [default: 1]")
+    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()
+
+    parser = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
+
+    # get occurrences of the transcripts
+    names        = dict()
+    progress = Progress(parser.getNbTranscripts(), "Reading names of %s" % (options.inputFileName), options.verbosity)
+    for transcript in parser.getIterator():
+        name = transcript.name
+        if name not in names:
+            names[name] = 1
+        else:
+            names[name] += 1
+        progress.inc()
+    progress.done()
+
+    # write output file
+    nbWritten = 0
+    writer        = Gff3Writer(options.outputFileName, options.verbosity)
+    if options.mysql:
+        mysqlWriter = MySqlTranscriptWriter(options.outputFileName, options.verbosity)
+    progress    = Progress(parser.getNbTranscripts(), "Writing transcripts", options.verbosity)
+    for transcript in parser.getIterator():
+        name = transcript.name
+        if names[name] <= options.occurrences:
+            nbWritten += 1
+            writer.addTranscript(transcript)
+            if options.mysql:
+                mysqlWriter.addTranscript(transcript)
+        progress.inc()
+    progress.done()
+                                                     
+    if options.mysql:
+        mysqlWriter.write()
+    print "%d input" % (parser.getNbTranscripts())
+    print "%d output (%.2f%%)" % (nbWritten, float(nbWritten) / parser.getNbTranscripts() * 100)