diff SMART/Java/Python/repetGffConverter.py @ 6:769e306b7933

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/repetGffConverter.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,71 @@
+#! /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.
+#
+"""Convert a GFF with REPET format to BED format"""
+
+import os
+from optparse import OptionParser
+from commons.core.parsing.GffParser import *
+from commons.core.writer.BedWriter import *
+from SMART.Java.Python.misc.Progress import *
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Repet GFF Convert v1.0.1: Convert REPET-flavored GFF to normal GFF. [Category: Personnal]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input",                        dest="inputFileName",    action="store",                                         type="string", help="input file [compulsory] [format: file in GFF3 format]")
+    parser.add_option("-o", "--output",                     dest="outputFileName", action="store",                                         type="string", help="output file [compulsory] [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            = GffParser(options.inputFileName, options.verbosity)
+    transcripts = dict()
+    progress        = Progress(parser.getNbTranscripts(), "Analyzing file %s" % (options.inputFileName), options.verbosity)
+    for transcript in parser.getIterator():
+        if transcript.feature.endswith("range"):
+            transcripts[transcript.name] = transcript
+        elif transcript.feature.endswith("hsp"):
+            if transcript.name in transcripts:
+                transcripts[transcript.name].addExon(transcript)
+            else:
+                sys.exit("Transcript %s is not defined\n" % (transcript.name))
+        else:
+            sys.exit("Do not understand feature %s" % (transcript.feature))
+        progress.inc()
+    progress.done()
+        
+    writer = BedWriter(options.outputFileName, options.verbosity)
+    for name in transcripts:
+        writer.addTranscript(transcripts[name])
+        
+    print "%d transcripts out of %d written (%.2f%%)" % (len(transcripts.keys()), parser.getNbTranscripts(), float(len(transcripts.keys())) / parser.getNbTranscripts() * 100)