--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/coordinatesToSequence.py	Thu May 02 09:56:47 2013 -0400
@@ -0,0 +1,64 @@
+#! /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 list of coordinates to sequences"""
+
+from optparse import OptionParser
+from commons.core.parsing.FastaParser import FastaParser
+from SMART.Java.Python.structure.TranscriptContainer import TranscriptContainer
+from commons.core.writer.FastaWriter import FastaWriter
+from SMART.Java.Python.misc.Progress import Progress
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Coordinates to Sequences v1.0.2: Extract the sequences from a list of coordinates. [Category: Conversion]"
+
+    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("-s", "--sequences", dest="sequences", action="store",  type="string", help="file that contains the sequences [compulsory] [format: file in FASTA format]")
+    parser.add_option("-o", "--output", dest="outputFileName", action="store",  default=None, type="string", help="output file (FASTA format) [format: output file in FASTA format]")
+    parser.add_option("-v", "--verbosity", dest="verbosity", action="store", default=1, type="int", help="trace level [format: int]")
+    (options, args) = parser.parse_args()
+
+    # create parser
+    parser = TranscriptContainer(options.inputFileName, options.format, options.verbosity) 
+
+    sequenceParser = FastaParser(options.sequences, options.verbosity)
+
+    writer = FastaWriter(options.outputFileName, options.verbosity)
+    progress = Progress(parser.getNbTranscripts(), "Reading %s" % (options.inputFileName), options.verbosity)
+    for transcript in parser.getIterator():
+        sequence = transcript.extractSequence(sequenceParser)
+        writer.addSequence(sequence)
+        progress.inc()
+    progress.done()