org.opencb.opencga.analysis.execution.plugins.ibs.IbsAnalysis.java Source code

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Here is the source code for org.opencb.opencga.analysis.execution.plugins.ibs.IbsAnalysis.java

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/*
 * Copyright 2015-2016 OpenCB
 *
 * 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 org.opencb.opencga.analysis.execution.plugins.ibs;

import org.apache.commons.lang3.StringUtils;
import org.opencb.biodata.tools.variant.algorithm.IdentityByState;
import org.opencb.biodata.tools.variant.algorithm.IdentityByStateClustering;
import org.opencb.commons.datastore.core.ObjectMap;
import org.opencb.commons.datastore.core.Query;
import org.opencb.commons.datastore.core.QueryOptions;
import org.opencb.opencga.analysis.execution.plugins.OpenCGAAnalysis;
import org.opencb.opencga.catalog.db.api.SampleDBAdaptor;
import org.opencb.opencga.catalog.managers.CatalogManager;
import org.opencb.opencga.catalog.models.Sample;
import org.opencb.opencga.catalog.models.tool.Execution;
import org.opencb.opencga.catalog.models.tool.Manifest;
import org.opencb.opencga.catalog.models.tool.Option;
import org.opencb.opencga.storage.core.variant.adaptors.VariantDBAdaptor;
import org.opencb.opencga.storage.core.variant.adaptors.VariantDBIterator;
import org.opencb.opencga.storage.core.variant.adaptors.VariantField;

import java.io.FileOutputStream;
import java.io.OutputStream;
import java.nio.file.Path;
import java.util.Arrays;
import java.util.Collections;
import java.util.List;
import java.util.Map;
import java.util.stream.Collectors;
import java.util.zip.GZIPOutputStream;

/**
 * Created on 26/11/15
 *
 * @author Jacobo Coll <jacobo167@gmail.com>
 */
public class IbsAnalysis extends OpenCGAAnalysis {

    public static final String OUTDIR = "outdir";
    public static final String SAMPLES = "samples";
    public static final String PLUGIN_ID = "ibs_plugin";
    private final Manifest manifest;

    public IbsAnalysis() {
        manifest = new Manifest(null, "0.1.0", PLUGIN_ID, "IBS plugin", "", "", "", null, Collections.emptyList(),
                Collections.singletonList(
                        new Execution("default", "default", "", Collections.emptyList(), Collections.emptyList(),
                                OUTDIR, Arrays.asList(new Option(OUTDIR, "", true), new Option(SAMPLES, "", false)),
                                Collections.emptyList(), null, null)),
                null, null);
    }

    @Override
    public Manifest getManifest() {
        return manifest;
    }

    @Override
    public String getIdentifier() {
        return PLUGIN_ID;
    }

    @Override
    public int run(Map<String, Path> input, Path outdir, ObjectMap params) throws Exception {
        CatalogManager catalogManager = getCatalogManager();
        String sessionId = getSessionId();
        long studyId = getStudyId();

        IdentityByStateClustering ibsc = new IdentityByStateClustering();
        List<String> samples;
        Query query = new Query(VariantDBAdaptor.VariantQueryParams.STUDIES.key(), studyId);
        QueryOptions options = new QueryOptions(QueryOptions.EXCLUDE, VariantField.ANNOTATION);

        Query samplesQuery = new Query();
        if (StringUtils.isNotEmpty(params.getString(SAMPLES))) {
            List<Long> sampleIds = catalogManager.getSampleIds(params.getString(SAMPLES), sessionId);
            samplesQuery.append(SampleDBAdaptor.QueryParams.ID.key(), sampleIds);
            query.append(VariantDBAdaptor.VariantQueryParams.RETURNED_SAMPLES.key(), sampleIds);
        }
        samples = catalogManager.getAllSamples(studyId, samplesQuery, new QueryOptions(), sessionId).getResult()
                .stream().map(Sample::getName).collect(Collectors.toList());

        List<IdentityByState> identityByStateList;
        try (VariantDBIterator iterator = getVariantStorageManager().iterable(sessionId).iterator(query, options)) {
            identityByStateList = ibsc.countIBS(iterator, samples);
        }
        if ("-".equals(outdir.getFileName().toString())) {
            ibsc.write(System.out, identityByStateList, samples);
        } else {
            Path outfile;
            if (outdir.toAbsolutePath().toFile().isDirectory()) {
                String alias = catalogManager.getStudy(studyId, sessionId).first().getAlias();
                outfile = outdir.resolve(alias + ".genome.gz");
            } else {
                outfile = outdir;
            }

            try (OutputStream outputStream = new GZIPOutputStream(new FileOutputStream(outfile.toFile()))) {
                ibsc.write(outputStream, identityByStateList, samples);
            }
        }

        return 0;
    }

}