diff smart_toolShed/SMART/Java/Python/splitByTag.py @ 0:e0f8dcca02ed

Uploaded S-MART tool. A toolbox manages RNA-Seq and ChIP-Seq data.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/splitByTag.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,68 @@
+#! /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.
+#
+"""Read a file and split it into several, depending on a tag"""
+
+import os
+from optparse import OptionParser
+from SMART.Java.Python.structure.TranscriptContainer import *
+from commons.core.writer.Gff3Writer import *
+from SMART.Java.Python.misc.Progress import *
+from SMART.Java.Python.misc import Utils
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Split By Tag v1.0.1: Read a file and split it into several, depending on a tag. [Category: Personnal]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input",                     dest="inputFileName",         action="store",                                        type="string", help="input file 1 [compulsory] [format: file in transcript format given by -f]")
+    parser.add_option("-f", "--format",                    dest="format",                        action="store",                                        type="string", help="format of file 1 [compulsory] [format: transcript file format]")
+    parser.add_option("-t", "--tag",                         dest="tag",                             action="store",                                        type="string", help="tag on which the split is made [compulsory] [format: string]")
+    parser.add_option("-o", "--output",                    dest="outputFileName",        action="store",                                        type="string", help="output file [format: output file in CSV format]")
+    parser.add_option("-v", "--verbosity",             dest="verbosity",                 action="store",            default=1,        type="int",        help="trace level [format: int]")
+    (options, args) = parser.parse_args()
+
+    transcriptContainer = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
+    writers                         = dict()
+
+    progress = Progress(transcriptContainer.getNbTranscripts(), "Reading file %s" % (options.inputFileName), options.verbosity)
+    for transcript in transcriptContainer.getIterator():
+        value = transcript.getTagValue(options.tag)
+        if value == None:
+            value = "noTag"
+        value = str(value).replace(" ", "_").title()
+        if value not in writers:
+            writers[value] = Gff3Writer("%s.gff3" % (os.path.join(options.outputFileName, value)))
+        writers[value].addTranscript(transcript)
+
+        progress.inc()
+    progress.done()