Java tutorial
/* * Copyright (C) 2014 Google Inc. * * 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 com.google.cloud.genomics.dataflow.pipelines; import com.google.cloud.dataflow.sdk.Pipeline; import com.google.cloud.dataflow.sdk.io.TextIO; import com.google.cloud.dataflow.sdk.options.Default; import com.google.cloud.dataflow.sdk.options.Description; import com.google.cloud.dataflow.sdk.options.PipelineOptionsFactory; import com.google.cloud.dataflow.sdk.transforms.Create; import com.google.cloud.dataflow.sdk.transforms.ParDo; import com.google.cloud.dataflow.sdk.values.PCollection; import com.google.cloud.genomics.dataflow.functions.SitesToShards; import com.google.cloud.genomics.dataflow.functions.pca.ExtractSimilarCallsets; import com.google.cloud.genomics.dataflow.functions.pca.OutputPCoAFile; import com.google.cloud.genomics.dataflow.readers.VariantStreamer; import com.google.cloud.genomics.dataflow.utils.GCSOutputOptions; import com.google.cloud.genomics.dataflow.utils.GenomicsOptions; import com.google.cloud.genomics.dataflow.utils.ShardOptions; import com.google.cloud.genomics.utils.GenomicsUtils; import com.google.cloud.genomics.utils.OfflineAuth; import com.google.cloud.genomics.utils.ShardBoundary; import com.google.cloud.genomics.utils.ShardUtils; import com.google.common.collect.BiMap; import com.google.common.collect.HashBiMap; import com.google.genomics.v1.StreamVariantsRequest; import java.io.IOException; import java.security.GeneralSecurityException; import java.util.Collections; import java.util.List; /** * A pipeline that generates similarity data for variants in a dataset. * * See http://googlegenomics.readthedocs.org/en/latest/use_cases/compute_principal_coordinate_analysis/index.html * for running instructions. */ public class VariantSimilarity { public static interface Options extends // Options for calculating over regions, chromosomes, or whole genomes. ShardOptions, // Options for calculating over a list of sites. SitesToShards.Options, // Options for the output destination. GCSOutputOptions { @Description("The ID of the Google Genomics variant set this pipeline is accessing. " + "Defaults to 1000 Genomes.") @Default.String("10473108253681171589") String getVariantSetId(); void setVariantSetId(String variantSetId); public static class Methods { public static void validateOptions(Options options) { GCSOutputOptions.Methods.validateOptions(options); } } } // Tip: Use the API explorer to test which fields to include in partial responses. // https://developers.google.com/apis-explorer/#p/genomics/v1/genomics.variants.stream?fields=variants(alternateBases%252Ccalls(callSetName%252Cgenotype)%252CreferenceBases)&_h=3&resource=%257B%250A++%2522variantSetId%2522%253A+%25223049512673186936334%2522%252C%250A++%2522referenceName%2522%253A+%2522chr17%2522%252C%250A++%2522start%2522%253A+%252241196311%2522%252C%250A++%2522end%2522%253A+%252241196312%2522%252C%250A++%2522callSetIds%2522%253A+%250A++%255B%25223049512673186936334-0%2522%250A++%255D%250A%257D& private static final String VARIANT_FIELDS = "variants(start,calls(genotype,callSetName))"; public static void main(String[] args) throws IOException, GeneralSecurityException { // Register the options so that they show up via --help PipelineOptionsFactory.register(Options.class); Options options = PipelineOptionsFactory.fromArgs(args).withValidation().as(Options.class); // Option validation is not yet automatic, we make an explicit call here. Options.Methods.validateOptions(options); OfflineAuth auth = GenomicsOptions.Methods.getGenomicsAuth(options); List<String> callSetNames = GenomicsUtils.getCallSetsNames(options.getVariantSetId(), auth); Collections.sort(callSetNames); // Ensure a stable sort order for reproducible results. BiMap<String, Integer> dataIndices = HashBiMap.create(); for (String callSetName : callSetNames) { dataIndices.put(callSetName, dataIndices.size()); } Pipeline p = Pipeline.create(options); p.begin(); PCollection<StreamVariantsRequest> requests; if (null != options.getSitesFilepath()) { // Compute PCA on a list of sites. requests = p.apply(TextIO.Read.named("ReadSites").from(options.getSitesFilepath())) .apply(new SitesToShards.SitesToStreamVariantsShardsTransform(options.getVariantSetId())); } else { List<StreamVariantsRequest> shardRequests = options.isAllReferences() ? ShardUtils.getVariantRequests(options.getVariantSetId(), ShardUtils.SexChromosomeFilter.EXCLUDE_XY, options.getBasesPerShard(), auth) : ShardUtils.getVariantRequests(options.getVariantSetId(), options.getReferences(), options.getBasesPerShard()); requests = p.apply(Create.of(shardRequests)); } requests.apply(new VariantStreamer(auth, ShardBoundary.Requirement.STRICT, VARIANT_FIELDS)) .apply(ParDo.of(new ExtractSimilarCallsets())) .apply(new OutputPCoAFile(dataIndices, options.getOutput())); p.run(); } }