--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/getIntrons.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.
+#
+from optparse import OptionParser
+from commons.core.parsing.ParserChooser import ParserChooser
+from commons.core.writer.TranscriptWriter import TranscriptWriter
+from SMART.Java.Python.structure.Transcript import Transcript
+from SMART.Java.Python.misc.Progress import Progress
+
+class GetIntrons(object):
+
+    def __init__(self, verbosity):
+        self.verbosity = verbosity
+
+    def setInputFile(self, fileName, format):
+        chooser = ParserChooser(self.verbosity)
+        chooser.findFormat(format)
+        self.parser = chooser.getParser(fileName)
+
+    def setOutputFile(self, fileName):
+        self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
+        
+    def run(self):
+        progress  = Progress(self.parser.getNbTranscripts(), "Reading input file", self.verbosity)
+        nbIntrons = 0
+        for cpt1, transcript in enumerate(self.parser.getIterator()):
+            for cpt2, intron in enumerate(transcript.getIntrons()):
+                intronTranscript = Transcript()
+                intronTranscript.copy(intron)
+                if "Parent" in intronTranscript.tags:
+                    del intronTranscript.tags["Parent"]
+                intronTranscript.tags["feature"] = "transcript"
+                if "ID" not in intronTranscript.tags or intronTranscript.tags["ID"] == "unnamed transcript":
+                    intronTranscript.tags["ID"] = "intron_%d-%d" % (cpt1+1, cpt2+1)
+                if intronTranscript.getName() == "unnamed transcript":
+                    intronTranscript.setName("intron_%d-%d" % (cpt1+1, cpt2+1))
+                self.writer.addTranscript(intronTranscript)
+                nbIntrons += 1
+            progress.inc()
+        self.writer.write()
+        self.writer.close()
+        progress.done()
+        if self.verbosity > 1:
+            print "%d transcripts read" % (self.parser.getNbTranscripts())
+            print "%d introns written" % (nbIntrons)
+
+
+if __name__ == "__main__":
+    
+    description = "Get Introns v1.0.1: Get the introns of a set of transcripts. [Category: Data Modification]"
+
+    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 file [compulsory] [format: transcript file format]")
+    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()
+
+    gi = GetIntrons(options.verbosity)
+    gi.setInputFile(options.inputFileName, options.format)
+    gi.setOutputFile(options.outputFileName)
+    gi.run()