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

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/changeTagName.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,90 @@
+#! /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.
+#
+"""
+Change the name of a tag
+"""
+
+import os
+import random
+from optparse import OptionParser
+from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+from SMART.Java.Python.misc.Progress import Progress
+from commons.core.writer.MySqlTranscriptWriter import MySqlTranscriptWriter
+from commons.core.writer.Gff3Writer import Gff3Writer
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Change Tag Name v1.0.1: Change the name of tag of a list 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", "--inputFormat", dest="inputFormat",    action="store",                      type="string", help="format of the input file [compulsory] [format: transcript file 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("-t", "--tag",         dest="tag",            action="store",                      type="string", help="name of the tag to change [compulsory] [format: string]")
+    parser.add_option("-n", "--name",        dest="name",           action="store",                      type="string", help="new name for the tag [compulsory] [format: string]")
+    parser.add_option("-y", "--mysql",       dest="mysql",          action="store_true", default=False,                 help="mySQL output [format: bool] [default: false]")    
+    parser.add_option("-v", "--verbosity",   dest="verbosity",      action="store",      default=1,      type="int",    help="trace level [format: int] [default: 1]")
+    parser.add_option("-l", "--log",         dest="log",            action="store_true", default=False,                 help="write a log file [format: bool] [default: false]")
+    (options, args) = parser.parse_args()
+
+    if options.log:
+        logHandle = open("%s.log" % options.outputFileName, "w")
+
+    # create parser and writer(s)
+    parser      = TranscriptContainer(options.inputFileName, options.inputFormat, options.verbosity)
+    tmpFileName = "tmpTranscriptFile%d.gff3" % (random.randint(0, 100000))
+    writer      = Gff3Writer(tmpFileName, options.verbosity)
+    if options.mysql:
+        mysqlWriter = MySqlTranscriptWriter(options.outputFileName, options.verbosity)
+    outputData = {}
+        
+    # process transcripts
+    progress = Progress(parser.getNbTranscripts(), "Printing transcripts %s" % (options.inputFileName), options.verbosity)
+    for transcript in parser.getIterator():
+        if options.tag in transcript.tags:
+            value = transcript.tags[options.tag]
+            del transcript.tags[options.tag]
+            transcript.tags[options.name] = value
+        writer.addTranscript(transcript)
+        if options.mysql:
+            mysqlWriter.addTranscript(transcript)
+        progress.inc()
+    progress.done()
+    parser.transcriptListParser.close()
+
+    writer.write()
+
+    if options.mysql:
+        mysqlWriter.write()
+
+    os.rename(tmpFileName, options.outputFileName)