001/*
002 *                    BioJava development code
003 *
004 * This code may be freely distributed and modified under the
005 * terms of the GNU Lesser General Public Licence.  This should
006 * be distributed with the code.  If you do not have a copy,
007 * see:
008 *
009 *      http://www.gnu.org/copyleft/lesser.html
010 *
011 * Copyright for this code is held jointly by the individual
012 * authors.  These should be listed in @author doc comments.
013 *
014 * For more information on the BioJava project and its aims,
015 * or to join the biojava-l mailing list, visit the home page
016 * at:
017 *
018 *      http://www.biojava.org/
019 *
020 */
021
022package org.biojava.nbio.genome.util;
023
024import org.biojava.nbio.core.sequence.DNASequence;
025import org.biojava.nbio.core.sequence.io.FastaReaderHelper;
026import org.biojava.nbio.core.sequence.io.FastaWriterHelper;
027import org.slf4j.Logger;
028import org.slf4j.LoggerFactory;
029
030import java.io.File;
031import java.util.ArrayList;
032import java.util.LinkedHashMap;
033
034
035/**
036 * Utility to write each Fasta entry to a unique file
037 * @author Scooter Willis <willishf at gmail dot com>
038 */
039public class SplitFasta {
040
041        private static final Logger logger = LoggerFactory.getLogger(SplitFasta.class);
042
043        public void processNucleotides(File fastaFileName,String uniqueid, File outputDirectory ) throws Exception{
044                if(!outputDirectory.exists())
045                        outputDirectory.mkdirs();
046
047                LinkedHashMap<String,DNASequence> dnaSequenceHashMap = FastaReaderHelper.readFastaDNASequence(fastaFileName);
048                for(DNASequence dnaSequence : dnaSequenceHashMap.values()){
049                        String fileName = outputDirectory.getAbsolutePath() + File.separatorChar;
050                        if(uniqueid.length() > 0){
051                                fileName = fileName + dnaSequence.getAccession().getID() + ".fna";
052                        }else{
053                                fileName = fileName + uniqueid + dnaSequence.getAccession().getID() + ".fna";
054                        }
055                        ArrayList<DNASequence> dnaList = new ArrayList<DNASequence>();
056                        dnaList.add(dnaSequence);
057                        FastaWriterHelper.writeNucleotideSequence(new File(fileName), dnaList);
058                }
059
060        }
061
062                public static void main( String[] args ){
063                try{
064                        SplitFasta splitFasta = new SplitFasta();
065                        splitFasta.processNucleotides(new File("/Users/Scooter/scripps/dyadic/analysis/454Scaffolds/454Scaffolds.fna"), "", new File("/Users/Scooter/scripps/dyadic/analysis/454Scaffolds/individual"));
066                }catch(Exception e){
067                        logger.error("Exception: ", e);
068                }
069        }
070
071}