# HG changeset patch
# User m-zytnicki
# Date 1391779788 18000
# Node ID 36eaa579fdb6623403769ae4afc000d410b6abca
# Parent  97aa2e42bfdfe3c18a1275c8618d6ffd440db494
Uploaded

diff -r 97aa2e42bfdf -r 36eaa579fdb6 SMART/Java/Python/RemoveExons.py
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/RemoveExons.py	Fri Feb 07 08:29:48 2014 -0500
@@ -0,0 +1,75 @@
+#! /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 RemoveExons(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 setOutputFile(self, fileName):
+		self.writer = TranscriptWriter(fileName, "gff3", self.verbosity)
+		
+	def run(self):
+		progress = Progress(self.parser.getNbTranscripts(), "Reading input file", self.verbosity)
+		for transcript in self.parser.getIterator():
+			transcript.removeExons()
+			self.writer.addTranscript(transcript)
+			progress.inc()
+		self.writer.write()
+		self.writer.close()
+		progress.done()
+
+if __name__ == "__main__":
+	
+	description = "Remove Exons v1.0.1: Excluse 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("-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()
+
+	re = RemoveExons(options.verbosity)
+	re.setInputFile(options.inputFileName, options.format)
+	re.setOutputFile(options.outputFileName)
+	re.run()
diff -r 97aa2e42bfdf -r 36eaa579fdb6 SMART/galaxy/.removeIntrons.xml.swp
Binary file SMART/galaxy/.removeIntrons.xml.swp has changed