--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/smart_toolShed/SMART/Java/Python/getElement.py	Thu Jan 17 10:52:14 2013 -0500
@@ -0,0 +1,106 @@
+#! /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.
+#
+"""Get the first element (exon / intron) from a list of transcripts"""
+
+import os
+from optparse import OptionParser
+from commons.core.writer.Gff3Writer import *
+from SMART.Java.Python.structure.TranscriptContainer import *
+from SMART.Java.Python.misc.Progress import *
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Get Element v1.0.1: Get the first element (exon / intron) from a list of transcripts. [Category: Personnal]"
+
+    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 [compulsory] [format: output file in GFF3 format]")
+    parser.add_option("-y", "--mysql",         dest="mysql",                    action="store_true", default=False,                                     help="mySQL output [format: bool] [default: false]")
+    parser.add_option("-t", "--type",            dest="type",                     action="store",                                                type="string", help="type of the element    [format: choice (exon, intron)]")
+    parser.add_option("-v", "--verbosity", dest="verbosity",            action="store",            default=1,                type="int",        help="trace level [format: int]")
+    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()
+
+    parser        = TranscriptContainer(options.inputFileName, options.format, options.verbosity)
+    writer        = Gff3Writer(options.outputFileName, options.verbosity)
+    sqlWriter = MySqlTranscriptWriter(options.outputFileName, options.verbosity)
+    
+    nbLines = parser.getNbTranscripts()
+    print "%i lines found" % (nbLines)
+
+    # treat transcripts
+    nbWritten = 0
+    nbUsed        = 0
+    progress    = Progress(nbLines, "Analyzing transcripts of " + options.inputFileName, options.verbosity)
+    for transcript in parser.getIterator():
+
+        outTranscript = Transcript()
+        outTranscript.setName(transcript.getName())
+        outTranscript.setDirection(transcript.getDirection())
+        outTranscript.setChromosome(transcript.getChromosome())
+        
+        if options.type == "exon":
+            if len(transcript.getExons()) > 1:
+                transcript.sortExons()
+                outTranscript.setStart(transcript.getExons()[0].getStart())
+                outTranscript.setEnd(transcript.getExons()[0].getEnd())
+                writer.addTranscript(outTranscript)
+                if options.mysql:
+                    sqlWriter.addTranscript(transcript)
+                nbWritten += 1
+                nbUsed        += 1
+        elif options.type == "intron":
+            used = False
+            for intron in transcript.getIntrons():
+                used = True
+                thisTranscript = Transcript()
+                thisTranscript.copy(outTranscript)
+                thisTranscript.setStart(intron.getStart())
+                thisTranscript.setEnd(intron.getEnd())
+                writer.addTranscript(thisTranscript)
+                if options.mysql:
+                    sqlWriter.addTranscript(transcript)
+                nbWritten += 1
+            if used:
+                nbUsed += 1
+        else:
+            sys.exit("Cannot understan type %s" % (options.type))
+        progress.inc()
+    progress.done()
+
+    if options.mysql:
+        sqlWriter.write()
+
+    print "nb sequences used: %d" % (nbUsed)
+    print "nb elements used: %d" % (nbWritten)