NormalizeFasta.java

package picard.reference;

import htsjdk.samtools.reference.ReferenceSequence;
import htsjdk.samtools.reference.ReferenceSequenceFile;
import htsjdk.samtools.reference.ReferenceSequenceFileFactory;
import htsjdk.samtools.util.IOUtil;
import htsjdk.samtools.util.Log;
import htsjdk.samtools.util.RuntimeIOException;
import picard.PicardException;
import picard.cmdline.CommandLineProgram;
import picard.cmdline.CommandLineProgramProperties;
import picard.cmdline.Option;
import picard.cmdline.programgroups.Fasta;
import picard.cmdline.StandardOptionDefinitions;

import java.io.BufferedWriter;
import java.io.File;
import java.io.IOException;

/**
 * Little program to "normalize" a fasta file to ensure that all line of sequence are the
 * same length, and are a reasonable length!
 */
@CommandLineProgramProperties(
        usage = NormalizeFasta.USAGE_SUMMARY + NormalizeFasta.USAGE_DETAILS,
        usageShort = NormalizeFasta.USAGE_SUMMARY,
        programGroup = Fasta.class
)
public class NormalizeFasta extends CommandLineProgram {
    static final String USAGE_SUMMARY = "Normalizes lines of sequence in a FASTA file to be of the same length.";
    static final String USAGE_DETAILS = "This tool takes any FASTA-formatted file and reformats the sequence to ensure that all of the " +
            "sequence record lines are of the same length (with the exception of the last line). Although the default setting is 100 bases " +
            "per line, a custom line_length can be specified by the user. In addition, record names can be truncated at the first " +
            "instance of a whitespace character to ensure downstream compatibility.<br />" +
            "<h4>Usage example:</h4>" +
            "<pre>" +
            "java -jar picard.jar NormalizeFasta \\<br />" +
            "      I=input_sequence.fasta \\<br />" +
            "      O=normalized_sequence.fasta" +
            "</pre>" +
            "<hr />"
            ;
    @Option(shortName= StandardOptionDefinitions.INPUT_SHORT_NAME, doc="The input FASTA file to normalize.")
    public File INPUT;

    @Option(shortName= StandardOptionDefinitions.OUTPUT_SHORT_NAME, doc="The output FASTA file to write.")
    public File OUTPUT;

    @Option(doc="The line length to be used for the output FASTA file.")
    public int LINE_LENGTH=100;

    @Option(doc="Truncate sequence names at first whitespace.")
    public boolean TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE=false;

    private final Log log = Log.getInstance(NormalizeFasta.class);

    public static void main(final String[] args) {
        new NormalizeFasta().instanceMainWithExit(args);
    }

    @Override
    protected int doWork() {
        IOUtil.assertFileIsReadable(INPUT);
        IOUtil.assertFileIsWritable(OUTPUT);

        if (INPUT.getAbsoluteFile().equals(OUTPUT.getAbsoluteFile())) {
            throw new IllegalArgumentException("Input and output cannot be the same file.");
        }

        final ReferenceSequenceFile ref = ReferenceSequenceFileFactory.getReferenceSequenceFile(INPUT, TRUNCATE_SEQUENCE_NAMES_AT_WHITESPACE);
        final BufferedWriter out = IOUtil.openFileForBufferedWriting(OUTPUT);

        ReferenceSequence seq = null;
        while ((seq = ref.nextSequence()) != null) {
            final String name  = seq.getName();
            final byte[] bases = seq.getBases();

            try {
                out.write(">");
                out.write(name);
                out.newLine();

                if (bases.length == 0) {
                    log.warn("Sequence " + name + " contains 0 bases.");
                }
                else {
                    for (int i=0; i<bases.length; ++i) {
                        if (i > 0 && i % LINE_LENGTH == 0) out.write("\n");
                        out.write(bases[i]);
                    }

                    out.write("\n");
                }
            }
            catch (IOException ioe) {
                throw new PicardException("Error writing to file " + OUTPUT.getAbsolutePath(), ioe);

            }
        }
        try {
            out.close();
        } catch (IOException e) {
            throw new RuntimeIOException(e);
        }
        return 0;
    }
}