uk.ac.ebi.eva.pipeline.jobs.steps.VepAnnotationGeneratorStep.java Source code

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Here is the source code for uk.ac.ebi.eva.pipeline.jobs.steps.VepAnnotationGeneratorStep.java

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/*
 * Copyright 2015-2016 EMBL - European Bioinformatics Institute
 *
 * Licensed under the Apache License, Version 2.0 (the "License");
 * you may not use this file except in compliance with the License.
 * You may obtain a copy of the License at
 *
 *      http://www.apache.org/licenses/LICENSE-2.0
 *
 * Unless required by applicable law or agreed to in writing, software
 * distributed under the License is distributed on an "AS IS" BASIS,
 * WITHOUT WARRANTIES OR CONDITIONS OF ANY KIND, either express or implied.
 * See the License for the specific language governing permissions and
 * limitations under the License.
 */
package uk.ac.ebi.eva.pipeline.jobs.steps;

import org.opencb.datastore.core.ObjectMap;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import org.springframework.batch.core.StepContribution;
import org.springframework.batch.core.configuration.annotation.StepScope;
import org.springframework.batch.core.scope.context.ChunkContext;
import org.springframework.batch.core.step.tasklet.Tasklet;
import org.springframework.batch.repeat.RepeatStatus;
import org.springframework.beans.factory.annotation.Autowired;
import org.springframework.context.annotation.Import;
import org.springframework.stereotype.Component;

import uk.ac.ebi.eva.pipeline.configuration.JobOptions;

import java.io.*;
import java.util.Arrays;
import java.util.zip.GZIPOutputStream;

/**
 *
 * @author Jose Miguel Mut Lopez <jmmut@ebi.ac.uk>
 * @author Cristina Yenyxe Gonzalez Garcia <cyenyxe@ebi.ac.uk>
 *
 * Tasklet that runs @see <a href="http://www.ensembl.org/info/docs/tools/vep/index.html">VEP</a> over a list of
 * coordinates of variants and nucleotide changes to determines the effect of the mutations.
 *
 * Input: file listing all the coordinates of variants and nucleotide changes like:
 *  20   60343   60343   G/A   +
 *  20   60419   60419   A/G   +
 *  20   60479   60479   C/T   +
 *  ...
 *
 * Output: file containing the VEP output
 *  20_60343_G/A   20:60343   A   -   -   -   intergenic_variant   -   -   -   -   -   -
 *  20_60419_A/G   20:60419   G   -   -   -   intergenic_variant   -   -   -   -   -   -
 *  20_60479_C/T   20:60479   T   -   -   -   intergenic_variant   -   -   -   -   -   rs149529999   GMAF=T:0.0018;AFR_MAF=T:0.01;AMR_MAF=T:0.0028
 *  ..
 */
@Component
@StepScope
@Import({ JobOptions.class })
public class VepAnnotationGeneratorStep implements Tasklet {
    private static final Logger logger = LoggerFactory.getLogger(VepAnnotationGeneratorStep.class);
    public static final String GENERATE_VEP_ANNOTATION = "Generate VEP annotation";

    @Autowired
    private JobOptions jobOptions;

    @Override
    public RepeatStatus execute(StepContribution contribution, ChunkContext chunkContext) throws Exception {
        ObjectMap pipelineOptions = jobOptions.getPipelineOptions();

        ProcessBuilder processBuilder = new ProcessBuilder("perl", pipelineOptions.getString("app.vep.path"),
                "--cache", "--cache_version", pipelineOptions.getString("app.vep.cache.version"), "-dir",
                pipelineOptions.getString("app.vep.cache.path"), "--species",
                pipelineOptions.getString("app.vep.cache.species"), "--fasta",
                pipelineOptions.getString("input.fasta"), "--fork", pipelineOptions.getString("app.vep.num-forks"),
                "-i", pipelineOptions.getString("vep.input"), "-o", "STDOUT", "--force_overwrite", "--offline",
                "--everything");

        logger.debug("VEP annotation parameters = " + Arrays.toString(processBuilder.command().toArray()));

        logger.info("Starting read from VEP output");
        Process process = processBuilder.start();

        long written = connectStreams(new BufferedInputStream(process.getInputStream()),
                new GZIPOutputStream(new FileOutputStream(pipelineOptions.getString("vep.output"))));

        int exitValue = process.waitFor();
        logger.info("Finishing read from VEP output, bytes written: " + written);

        if (exitValue > 0) {
            String errorLog = pipelineOptions.getString("vep.output") + ".errors.txt";
            connectStreams(new BufferedInputStream(process.getErrorStream()), new FileOutputStream(errorLog));
            throw new Exception("Error while running VEP (exit status " + exitValue + "). See " + errorLog
                    + " for the errors description from VEP.");
        }

        return RepeatStatus.FINISHED;
    }

    /**
     * read all the inputStream and write it into the outputStream
     *
     * TODO: optimize with buffers?
     * @throws IOException
     */
    private long connectStreams(InputStream inputStream, OutputStream outputStream) throws IOException {
        int read = inputStream.read();
        long written = 0;
        while (read != -1) {
            written++;
            outputStream.write(read);
            read = inputStream.read();
        }

        outputStream.close();
        inputStream.close();
        return written;
    }
}