+// $Id:
+// FORESTER -- software libraries and applications
+// for evolutionary biology research and applications.
+//
+// Copyright (C) 2008-2009 Christian M. Zmasek
+// Copyright (C) 2008-2009 Burnham Institute for Medical Research
+// All rights reserved
+//
+// This library is free software; you can redistribute it and/or
+// modify it under the terms of the GNU Lesser General Public
+// License as published by the Free Software Foundation; either
+// version 2.1 of the License, or (at your option) any later version.
+//
+// This library is distributed in the hope that it will be useful,
+// but WITHOUT ANY WARRANTY; without even the implied warranty of
+// MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the GNU
+// Lesser General Public License for more details.
+//
+// You should have received a copy of the GNU Lesser General Public
+// License along with this library; if not, write to the Free Software
+// Foundation, Inc., 51 Franklin Street, Fifth Floor, Boston, MA 02110-1301, USA
+//
+// Contact: phylosoft @ gmail . com
+// WWW: https://sites.google.com/site/cmzmasek/home/software/forester
+//
+//
+// "java -Xmx1024m -cp path\to\forester.jar org.forester.application.fasta_split
+//
+//
+
+package org.forester.application;
+
+import java.io.File;
+import java.io.FileInputStream;
+import java.io.FileNotFoundException;
+import java.io.IOException;
+import java.util.ArrayList;
+import java.util.HashMap;
+import java.util.List;
+import java.util.Map;
+import java.util.regex.Matcher;
+import java.util.regex.Pattern;
+
+import org.forester.io.parsers.FastaParser;
+import org.forester.io.writers.SequenceWriter;
+import org.forester.io.writers.SequenceWriter.SEQ_FORMAT;
+import org.forester.sequence.BasicSequence;
+import org.forester.sequence.MolecularSequence;
+import org.forester.util.CommandLineArguments;
+import org.forester.util.ForesterUtil;
+
+public final class rename_fasta {
+
+
+
+ public static void main( final String args[] ) {
+ try {
+ final File infile = new File( args[ 0 ] );
+ final File outfile = new File( args[ 1 ] );
+ List<MolecularSequence> seqs;
+ seqs = FastaParser.parse( new FileInputStream( infile ) );
+ for( MolecularSequence seq : seqs ) {
+ BasicSequence bseq = ( BasicSequence ) seq;
+ final int i = bseq.getIdentifier().lastIndexOf( '_' );
+ if ( i > 0 ) {
+ bseq.setIdentifier( bseq.getIdentifier().substring( i + 1 ) );
+ }
+ }
+ SequenceWriter.writeSeqs( seqs, outfile, SEQ_FORMAT.FASTA, 60 );
+ }
+ catch ( FileNotFoundException e ) {
+ e.printStackTrace();
+ }
+ catch ( IOException e ) {
+ e.printStackTrace();
+ }
+ }
+
+
+}