--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/txtToFasta.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,63 @@
+#! /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.
+#
+"""Transform a plain text file to a FASTA file"""
+
+import os
+from optparse import OptionParser
+from SMART.Java.Python.structure.Sequence import *
+from SMART.Java.Python.misc.Progress import *
+
+
+if __name__ == "__main__":
+    
+    # parse command line
+    parser = OptionParser()
+    description = "Txt to Fasta v1.0.1: Convert a Txt file (one sequence per line) into Fasta file. [Category: Personnal]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input",     dest="inputFileName",  action="store",            type="string", help="input file [compulsory] [format: file in TXT format]")
+    parser.add_option("-o", "--output",    dest="outputFileName", action="store",            type="string", help="output file [compulsory] [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()
+
+    inputFile = open(options.inputFileName)
+    outputFile = open(options.outputFileName, "w")
+    
+    for line in inputFile:
+        line = line.strip()
+        splittedLine = line.split()
+        sequence = splittedLine[0]
+        nb = 1 if len(splittedLine) == 1 else int(splittedLine[1])
+        for i in range(nb):
+            outputFile.write(">%s\n%s\n" % (sequence, sequence))
+    
+    inputFile.close()
+    outputFile.close()