--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/restrictTranscriptList.py	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,85 @@
+#! /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.
+#
+"""Restrict a transcript list with some parameters (regions)"""
+
+from optparse import OptionParser
+from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+from commons.core.writer.TranscriptWriter import TranscriptWriter
+from SMART.Java.Python.misc.Progress import Progress
+
+STRAND2DIRECTION = {"+": 1, "-": -1, None: None}
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Restrict Transcript List v1.0.2: Keep the coordinates which are located in a given position. [Category: Data Selection]"
+
+    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 [compulsory] [format: transcript file format]")
+    parser.add_option("-c", "--chromosome", dest="chromosome",     action="store",            default=None,    type="string", help="chromosome [format: string]")
+    parser.add_option("-s", "--start",      dest="start",          action="store",            default=None,    type="int",    help="start [format: int]")
+    parser.add_option("-e", "--end",        dest="end",            action="store",            default=None,    type="int",    help="end [format: int]")
+    parser.add_option("-t", "--strand",     dest="strand",         action="store",            default=None,    type="string", help="strand (+ or -) [format: string]")
+    parser.add_option("-o", "--output",     dest="outputFileName", action="store",                             type="string", help="output file [format: output file in GFF3 format]")
+    parser.add_option("-v", "--verbosity",  dest="verbosity",      action="store",            default=1,       type="int",    help="trace level [format: int]")
+    (options, args) = parser.parse_args()
+
+    parser = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
+    writer = TranscriptWriter(options.outputFileName, options.format, options.verbosity)
+
+    direction = STRAND2DIRECTION[options.strand]
+        
+    nbTranscripts = parser.getNbTranscripts()
+    progress      = Progress(nbTranscripts, "Parsing file %s" % (options.inputFileName), options.verbosity)
+    
+    nbTotal = 0
+    nbKept    = 0
+    for transcript in parser.getIterator():
+        progress.inc()
+        nbTotal += 1
+        if options.chromosome != None and options.chromosome != transcript.getChromosome():
+            continue
+        if options.start != None and options.start > transcript.getEnd():
+            continue
+        if options.end != None and options.end < transcript.getStart():
+            continue
+        if options.end != None and options.end < transcript.getStart():
+            continue
+        if direction != None and direction != transcript.getDirection():
+            continue
+        nbKept += 1
+        writer.addTranscript(transcript)
+    progress.done()
+    
+    writer.write()
+        
+    print "%d out of %d are kept (%f%%)" % (nbKept, nbTotal, (float(nbKept) / nbTotal * 100))