demo.ParseFastaFileDemo Maven / Gradle / Ivy

Go to download
Show more of this group Show more artifacts with this name
Show all versions of biojava-core Show documentation
There is a newer version: 7.2.2
/*
 *                    BioJava development code
 *
 * This code may be freely distributed and modified under the
 * terms of the GNU Lesser General Public Licence.  This should
 * be distributed with the code.  If you do not have a copy,
 * see:
 *
 *      http://www.gnu.org/copyleft/lesser.html
 *
 * Copyright for this code is held jointly by the individual
 * authors.  These should be listed in @author doc comments.
 *
 * For more information on the BioJava project and its aims,
 * or to join the biojava-l mailing list, visit the home page
 * at:
 *
 *      http://www.biojava.org/
 *
 */
package demo;


import java.io.File;
import java.io.InputStream;
import java.util.LinkedHashMap;
import java.util.logging.Level;
import java.util.logging.Logger;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
import org.biojava.nbio.core.sequence.io.FastaReader;
import org.biojava.nbio.core.sequence.io.GenericFastaHeaderParser;
import org.biojava.nbio.core.sequence.io.ProteinSequenceCreator;
import org.biojava.nbio.core.util.InputStreamProvider;


/**
 * Created by andreas on 6/17/15.
 */
public class ParseFastaFileDemo {


	public ParseFastaFileDemo(){


		}

	/** e.g. download ftp://ftp.uniprot.org/pub/databases/uniprot/current_release/knowledgebase/complete/uniprot_trembl.fasta.gz
	 * and pass in path to local location of file
	 *
	 * @param args
	 */
		public static void main(String[] args) {

			int mb = 1024*1024;

			//Getting the runtime reference from system
			Runtime runtime = Runtime.getRuntime();

			System.out.println("##### Heap utilization statistics [MB] #####");

			//Print used memory
			System.out.println("Used Memory:"
					+ (runtime.totalMemory() - runtime.freeMemory()) / mb);

			//Print free memory
			System.out.println("Free Memory:"
					+ runtime.freeMemory() / mb);

			//Print total available memory
			System.out.println("Total Memory:" + runtime.totalMemory() / mb);

			//Print Maximum available memory
			System.out.println("Max Memory:" + runtime.maxMemory() / mb);


			if ( args.length < 1) {
				System.err.println("First argument needs to be path to fasta file");
				return;
			}

			File f = new File(args[0]);

			if ( ! f.exists()) {
				System.err.println("File does not exist " + args[0]);
				return;
			}

			long timeS = System.currentTimeMillis();

			try {

				// automatically uncompress files using InputStreamProvider
				InputStreamProvider isp = new InputStreamProvider();

				InputStream inStream = isp.getInputStream(f);


				FastaReader fastaReader = new FastaReader(
						inStream,
						new GenericFastaHeaderParser(),
						new ProteinSequenceCreator(AminoAcidCompoundSet.getAminoAcidCompoundSet()));

				LinkedHashMap b;

				int nrSeq = 0;

				while ((b = fastaReader.process(100)) != null) {
					for (String key : b.keySet()) {
						nrSeq++;
						//System.out.println(nrSeq + " : " + key + " " + b.get(key));
						if ( nrSeq % 100000 == 0)
							System.out.println(nrSeq );
					}

				}
				long timeE = System.currentTimeMillis();
				System.out.println("parsed a total of " + nrSeq + " TREMBL sequences! in " + (timeE - timeS));
			} catch (Exception ex) {
				Logger.getLogger(ParseFastaFileDemo.class.getName()).log(Level.SEVERE, null, ex);
			}
		}
}