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Google Genomics Dataflow pipelines.
/*
* Copyright (C) 2016 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.options.Validation.Required;
import com.google.cloud.dataflow.sdk.transforms.Create;
import com.google.cloud.dataflow.sdk.transforms.DoFn;
import com.google.cloud.dataflow.sdk.transforms.ParDo;
import com.google.cloud.dataflow.sdk.values.PCollection;
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.OfflineAuth;
import com.google.cloud.genomics.utils.ShardBoundary;
import com.google.cloud.genomics.utils.ShardUtils;
import com.google.common.base.CharMatcher;
import com.google.common.base.Joiner;
import com.google.common.base.Splitter;
import com.google.common.collect.ImmutableSet;
import com.google.common.io.Files;
import com.google.genomics.v1.StreamVariantsRequest;
import com.google.genomics.v1.Variant;
import com.google.genomics.v1.VariantCall;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.File;
import java.io.IOException;
import java.nio.charset.Charset;
import java.security.GeneralSecurityException;
import java.util.List;
/**
* Given a list of callset ids, identify variants that are associated only with the specified
* individuals (i.e. variants private to those individuals).
*
* This pipeline might be used in combination with the DeleteVariants pipeline to, for example,
* remove all variants private to a particular family from the variant set.
*/
public class IdentifyPrivateVariants {
public static interface Options extends
// Options for calculating over regions, chromosomes, or whole genomes.
ShardOptions,
// Options for the output destination.
GCSOutputOptions {
@Description("The ID of the Google Genomics variant set from which this pipeline "
+ "will identify private variants.")
@Required
String getVariantSetId();
void setVariantSetId(String variantSetId);
@Description("A local file path to a list of newline-separated callset IDs. "
+ "Any variants private to those callset IDs will be deleted.")
@Required
String getCallSetIdsFilepath();
void setCallSetIdsFilepath(String filepath);
@Description("Whether variants with no callsets should also be identified. Defaults to false.")
@Default.Boolean(false)
boolean getIdentifyVariantsWithoutCalls();
void setIdentifyVariantsWithoutCalls(boolean identifyVariantsWithoutCalls);
public static class Methods {
public static void validateOptions(Options options) {
GCSOutputOptions.Methods.validateOptions(options);
}
}
}
private static final Logger LOG = LoggerFactory.getLogger(IdentifyPrivateVariants.class);
// 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(id,reference_name,start,end,reference_bases,alternate_bases,calls(callSetId))";
/**
* Pipeline function implementing a filter only returning variants private to one or more callset
* IDs and optionally those with no callsetIds.
*/
public static final class PrivateVariantsFilterFn extends DoFn {
private final ImmutableSet callSetIds;
private boolean retainVariantsWithNoCalls;
/**
* @param callSetIds
*/
public PrivateVariantsFilterFn(ImmutableSet callSetIds,
boolean retainVariantsWithNoCalls) {
super();
this.callSetIds = callSetIds;
this.retainVariantsWithNoCalls = retainVariantsWithNoCalls;
}
@Override
public void processElement(ProcessContext context) {
Variant variant = context.element();
List calls = variant.getCallsList();
for (VariantCall call : calls) {
if (!callSetIds.contains(call.getCallSetId())) {
// We found a callset ID not in our set. This variant is not private
// to our set of callset IDs. Skip it.
return;
}
}
if (!retainVariantsWithNoCalls && calls.isEmpty()) {
// This is a variant with no calls. Skip it.
return;
}
context.output(variant);
}
}
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);
// Grab and parse the list of callset IDs.
String fileContents =
Files.toString(new File(options.getCallSetIdsFilepath()), Charset.defaultCharset());
ImmutableSet callSetIds =
ImmutableSet
.builder()
.addAll(
Splitter.on(CharMatcher.breakingWhitespace()).omitEmptyStrings().trimResults()
.split(fileContents)).build();
LOG.info("The pipeline will identify and write to Cloud Storage variants "
+ "private to " + callSetIds.size() + " genomes with callSetIds: " + callSetIds);
if (options.getIdentifyVariantsWithoutCalls()) {
LOG.info("* The pipeline will also identify variants with no callsets. *");
}
List shardRequests =
options.isAllReferences() ? ShardUtils.getVariantRequests(options.getVariantSetId(),
ShardUtils.SexChromosomeFilter.INCLUDE_XY, options.getBasesPerShard(), auth)
: ShardUtils.getVariantRequests(options.getVariantSetId(), options.getReferences(),
options.getBasesPerShard());
Pipeline p = Pipeline.create(options);
PCollection variants = p.begin()
.apply(Create.of(shardRequests))
.apply(new VariantStreamer(auth, ShardBoundary.Requirement.STRICT, VARIANT_FIELDS))
.apply(ParDo.of(new PrivateVariantsFilterFn(callSetIds,
options.getIdentifyVariantsWithoutCalls())));
variants.apply(ParDo.named("FormatResults").of(new DoFn() {
@Override
public void processElement(ProcessContext c) {
Variant v = c.element();
c.output(Joiner.on("\t").join(v.getId(),
v.getReferenceName(),
v.getStart(),
v.getEnd(),
v.getReferenceBases(),
Joiner.on(",").join(v.getAlternateBasesList())
));
}
}))
.apply(TextIO.Write.to(options.getOutput()));
p.run();
}
}
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