--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/getExons.py	Thu Jan 17 10:52:14 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.
+#
+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
+
+zeroBaseToOneBaseConvertor = (lambda x: x - 1 if x > 0 else x)
+
+class GetExons(object):
+
+    def __init__(self, verbosity):
+        self.verbosity = verbosity
+        self.selection = False
+
+    def setInputFile(self, fileName, format):
+        chooser = ParserChooser(self.verbosity)
+        chooser.findFormat(format)
+        self.parser = chooser.getParser(fileName)
+
+    def setSelection(self, selection):
+        if selection == None:
+            return
+        self.selection = True
+        self.selectionItems = []
+        self.selectionIntervals = []
+        for part in selection.split(","):
+            try:
+                splittedPart = map(int, part.split(".."))
+            except Exception:
+                raise Exception("Elements '" + splittedPart + "' of selection '" + selection + "' do no seem to be integers!")
+            if len(splittedPart) == 1:
+                self.selectionItems.append(splittedPart[0])
+            elif len(splittedPart) == 2:
+                self.selectionIntervals.append((splittedPart[0], splittedPart[1]))
+            else:
+                raise Exception("Cannot parse elements '" + splittedPart + "' of selection '" + selection + "'!")
+
+    def getSelectionExonIndices(self, nbExons):
+        if not self.selection:
+            return range(nbExons)
+        indices = []
+        for item in self.selectionItems:
+            indices.append(range(nbExons)[zeroBaseToOneBaseConvertor(item)])
+        for start, end in self.selectionIntervals:
+            start, end = map(zeroBaseToOneBaseConvertor, (start, end))
+            if end > 0:
+                end += 1
+            indices.extend(range(nbExons)[start:end])
+        return indices
+
+    def setOutputFile(self, fileName):
+        self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
+        
+    def run(self):
+        progress = Progress(self.parser.getNbTranscripts(), "Reading input file", self.verbosity)
+        nbExons = 0
+        for cpt1, transcript in enumerate(self.parser.getIterator()):
+            selectedExons = self.getSelectionExonIndices(transcript.getNbExons())
+            transcript.sortExons()
+            for cpt2, exon in enumerate(transcript.getExons()):
+                if cpt2 not in selectedExons:
+                    continue
+                exonTranscript = Transcript()
+                exonTranscript.copy(exon)
+                if "Parent" in exonTranscript.tags:
+                    del exonTranscript.tags["Parent"]
+                exonTranscript.tags["feature"] = "transcript"
+                if "ID" not in exonTranscript.tags or exonTranscript.tags["ID"] == "unnamed transcript":
+                    exonTranscript.tags["ID"] = "exon_%d-%d" % (cpt1+1, cpt2+1)
+                if exonTranscript.getName() == "unnamed transcript":
+                    exonTranscript.setName("exon_%d-%d" % (cpt1+1, cpt2+1))
+                self.writer.addTranscript(exonTranscript)
+                nbExons += 1
+            progress.inc()
+        self.writer.write()
+        self.writer.close()
+        progress.done()
+        if self.verbosity > 1:
+            print "%d transcripts read" % (self.parser.getNbTranscripts())
+            print "%d exons written" % (nbExons)
+
+if __name__ == "__main__":
+    
+    description = "Get Exons v1.0.1: Get the exons 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("-s", "--select",    dest="select",         action="store", default=None, type="string", help="select some of the exons (like '1,2,5..-3,-1') [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()
+
+    ge = GetExons(options.verbosity)
+    ge.setInputFile(options.inputFileName, options.format)
+    ge.setSelection(options.select)
+    ge.setOutputFile(options.outputFileName)
+    ge.run()