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

Change the repository level.

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/Java/Python/getSequence.py	Fri Jan 18 04:54:14 2013 -0500
@@ -0,0 +1,60 @@
+#! /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 a given sequence in a multi-Fasta file"""
+import sys
+from optparse import OptionParser
+from commons.core.parsing.FastaParser import FastaParser
+from SMART.Java.Python.misc.Progress import Progress
+from commons.core.writer.FastaWriter import FastaWriter
+
+if __name__ == "__main__":
+    
+    # parse command line
+    description = "Get Sequence v1.0.1: Get a single sequence in a FASTA file. [Category: Data Selection]"
+
+    parser = OptionParser(description = description)
+    parser.add_option("-i", "--input", dest="inputFileName",action="store",type="string", help="multi-FASTA file [compulsory] [format: file in FASTA format]")
+    parser.add_option("-n", "--name",dest="name",action="store",type="string", help="name of the sequence [compulsory] [format: string]")
+    parser.add_option("-o", "--output",dest="outputFileName",action="store",type="string", help="output sequence file (FASTA) [compulsory] [format: 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()
+
+    # read Fasta file
+    sequenceListParser = FastaParser(options.inputFileName, options.verbosity)
+    for sequence in sequenceListParser.getIterator():
+        name = sequence.name.split(" ")[0]
+        if name == options.name:
+            writer = FastaWriter(options.outputFileName, options.verbosity)
+            writer.addSequence(sequence)
+            print sequence.printFasta(),
+            sys.exit(0)
+    writer.close()
+    print "No sequence found"