org.dishevelled.bio.tools.EnsemblVariantTableToVcf.java Source code

Introduction

Here is the source code for org.dishevelled.bio.tools.EnsemblVariantTableToVcf.java

Source

/*
    
dsh-bio-tools  Command line tools.
Copyright (c) 2013-2019 held jointly by the individual authors.
    
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 3 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; with out 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., 59 Temple Place, Suite 330, Boston, MA 02111-1307  USA.
    
> http://www.fsf.org/licensing/licenses/lgpl.html
> http://www.opensource.org/licenses/lgpl-license.php
    
*/
package org.dishevelled.bio.tools;

import static org.dishevelled.compress.Readers.reader;
import static org.dishevelled.compress.Writers.writer;

import java.io.BufferedReader;
import java.io.File;
import java.io.PrintWriter;

import java.util.Collections;
import java.util.List;

import java.util.concurrent.Callable;

import org.apache.commons.csv.CSVFormat;
import org.apache.commons.csv.CSVRecord;

import org.dishevelled.bio.variant.vcf.VcfHeader;
import org.dishevelled.bio.variant.vcf.VcfRecord;
import org.dishevelled.bio.variant.vcf.VcfSample;
import org.dishevelled.bio.variant.vcf.VcfWriter;

import org.dishevelled.commandline.ArgumentList;
import org.dishevelled.commandline.CommandLine;
import org.dishevelled.commandline.CommandLineParseException;
import org.dishevelled.commandline.CommandLineParser;
import org.dishevelled.commandline.Switch;
import org.dishevelled.commandline.Usage;

import org.dishevelled.commandline.argument.FileArgument;

/**
 * Convert Ensembl variant table to VCF format.
 *
 * @author  Michael Heuer
 */
public class EnsemblVariantTableToVcf implements Callable<Integer> {
    private final File inputEnsemblVariantTableFile;
    private final File outputVcfFile;
    private static final String USAGE = "dsh-variant-table-to-vcf [args]";

    /**
     * Convert Ensembl variant table to VCF format
     *
     * @param inputEnsemblVariantTableFile input Ensembl variant table file, if any
     * @param outputVcfFile output VCF file, if any
     */
    public EnsemblVariantTableToVcf(final File inputEnsemblVariantTableFile, final File outputVcfFile) {
        this.inputEnsemblVariantTableFile = inputEnsemblVariantTableFile;
        this.outputVcfFile = outputVcfFile;
    }

    @Override
    public Integer call() throws Exception {
        BufferedReader reader = null;
        PrintWriter writer = null;
        try {
            reader = reader(inputEnsemblVariantTableFile);
            writer = writer(outputVcfFile);

            VcfHeader header = VcfHeader.builder().withFileFormat("VCFv4.2").withMeta("##fileformat=VCFv4.2")
                    .build();
            VcfWriter.writeHeader(header, writer);

            List<VcfSample> samples = Collections.emptyList();
            VcfWriter.writeColumnHeader(samples, writer);

            VcfRecord.Builder builder = VcfRecord.builder().withFilter("PASS").withFormat("");

            for (CSVRecord record : CSVFormat.DEFAULT.withHeader().parse(reader)) {
                String variantId = record.get("Variant ID");
                String[] location = record.get("Location").split(":");
                String[] alleles = record.get("Alleles").replace("-", ".").split("/");

                if (alleles.length != 2) {
                    // log warning, found e.g. COSMIC_MUTATION, HGMD_MUTATION, or CCC/-/CC, G/A/C/T
                    continue;
                }
                VcfRecord vcfRecord = builder.withChrom(location[0]).withPos(Long.parseLong(location[1]))
                        .withRef(alleles[0]).withAlt(alleles[1]).withId(variantId).build();

                VcfWriter.writeRecord(samples, vcfRecord, writer);
            }
            return 0;
        } finally {
            try {
                reader.close();
            } catch (Exception e) {
                // ignore
            }
            try {
                writer.close();
            } catch (Exception e) {
                // ignore
            }
        }
    }

    /**
     * Main.
     *
     * @param args command line args
     */
    public static void main(final String[] args) {
        Switch about = new Switch("a", "about", "display about message");
        Switch help = new Switch("h", "help", "display help message");
        FileArgument inputEnsemblVariantTableFile = new FileArgument("i", "input-variant-table-file",
                "input Ensembl variant table file, default stdin", false);
        FileArgument outputVcfFile = new FileArgument("o", "output-vcf-file", "output VCF file, default stdout",
                false);

        ArgumentList arguments = new ArgumentList(about, help, inputEnsemblVariantTableFile, outputVcfFile);
        CommandLine commandLine = new CommandLine(args);

        EnsemblVariantTableToVcf ensemblVariantTableToVcf = null;
        try {
            CommandLineParser.parse(commandLine, arguments);
            if (about.wasFound()) {
                About.about(System.out);
                System.exit(0);
            }
            if (help.wasFound()) {
                Usage.usage(USAGE, null, commandLine, arguments, System.out);
                System.exit(0);
            }
            ensemblVariantTableToVcf = new EnsemblVariantTableToVcf(inputEnsemblVariantTableFile.getValue(),
                    outputVcfFile.getValue());
        } catch (CommandLineParseException e) {
            if (about.wasFound()) {
                About.about(System.out);
                System.exit(0);
            }
            if (help.wasFound()) {
                Usage.usage(USAGE, null, commandLine, arguments, System.out);
                System.exit(0);
            }
            Usage.usage(USAGE, e, commandLine, arguments, System.err);
            System.exit(-1);
        } catch (IllegalArgumentException e) {
            Usage.usage(USAGE, e, commandLine, arguments, System.err);
            System.exit(-1);
        }
        try {
            System.exit(ensemblVariantTableToVcf.call());
        } catch (Exception e) {
            e.printStackTrace();
            System.exit(1);
        }
    }
}