Move all MongoDB files into private/java/src/org/broadinstitute/sting/mongodb
This commit is contained in:
Joel Thibault
parent
bdf6d1f109
commit
4d732fa586
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@ -1,121 +0,0 @@
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package org.broadinstitute.sting.gatk.walkers;
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/**
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* Created with IntelliJ IDEA.
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* User: thibault
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* Date: 3/30/12
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* Time: 4:47 PM
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* To change this template use File | Settings | File Templates.
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*/
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import com.mongodb.BasicDBObject;
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import com.mongodb.DBCollection;
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import org.broad.tribble.Feature;
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import org.broadinstitute.sting.commandline.Input;
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import org.broadinstitute.sting.commandline.Output;
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import org.broadinstitute.sting.commandline.RodBinding;
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import org.broadinstitute.sting.gatk.contexts.AlignmentContext;
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import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.db.MongoDB;
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import org.broadinstitute.sting.utils.variantcontext.VariantContext;
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import java.io.File;
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import java.io.PrintStream;
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import java.util.Collection;
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import java.util.List;
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/**
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* Inserts all of the RODs in the input data set. Data is inserted using VariantContext.toMongoDB().
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*/
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public class InsertRODsWalker extends RodWalker<Integer, Integer> {
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@Input(fullName="input", shortName = "input", doc="The input ROD which should be inserted into the DB.", required=true)
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public RodBinding<Feature> input;
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@Output
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PrintStream out;
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private String RODFileName;
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@Override
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public void initialize() {
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DBCollection mongoAttributes = MongoDB.getAttributesCollection();
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DBCollection mongoSamples = MongoDB.getSamplesCollection();
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RODFileName = input.getSource();
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int lastSep = RODFileName.lastIndexOf(File.separator);
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RODFileName = RODFileName.substring(lastSep + 1);
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// set up indices
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mongoAttributes.ensureIndex("location");
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mongoAttributes.ensureIndex("sourceROD");
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mongoAttributes.ensureIndex("contig");
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mongoAttributes.ensureIndex("start");
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mongoAttributes.ensureIndex("stop");
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mongoSamples.ensureIndex("location");
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mongoSamples.ensureIndex("sample");
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mongoSamples.ensureIndex("sourceROD");
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mongoSamples.ensureIndex("contig");
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mongoSamples.ensureIndex("start");
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mongoSamples.ensureIndex("stop");
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// set up primary keys
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mongoAttributes.ensureIndex(new BasicDBObject("location", 1).append("sourceROD", 1).append("alleles", 1), new BasicDBObject("unique", 1));
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mongoSamples.ensureIndex(new BasicDBObject("location", 1).append("sourceROD", 1).append("alleles", 1).append("sample", 1), new BasicDBObject("unique", 1));
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}
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/**
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* Initialize the number of loci processed to zero.
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*
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* @return 0
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*/
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public Integer reduceInit() { return 0; }
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/**
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*
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* @param tracker the meta-data tracker
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* @param ref the reference base
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* @param context the context for the given locus
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* @return 1 if the locus was successfully processed, 0 if otherwise
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*/
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( tracker == null )
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return 0;
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DBCollection mongoAttributes = MongoDB.getAttributesCollection();
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DBCollection mongoSamples = MongoDB.getSamplesCollection();
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for ( Feature feature : tracker.getValues(Feature.class, context.getLocation()) ) {
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if ( feature instanceof VariantContext ) {
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VariantContext vc = (VariantContext) feature;
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Pair<BasicDBObject,List<BasicDBObject>> mongoCollections = vc.toMongoDB(RODFileName);
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mongoAttributes.insert(mongoCollections.first);
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for (BasicDBObject sampleForMongo : mongoCollections.second) {
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mongoSamples.insert(sampleForMongo);
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}
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}
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}
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return 1;
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}
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/**
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* Increment the number of rods processed.
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*
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* @param value result of the map.
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* @param sum accumulator for the reduce.
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* @return the new number of rods processed.
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*/
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public Integer reduce(Integer value, Integer sum) {
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return sum + value;
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}
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public void onTraversalDone(Integer result) {
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MongoDB.close();
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}
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}
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@ -24,10 +24,6 @@
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package org.broadinstitute.sting.gatk.walkers.variantutils;
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import com.mongodb.BasicDBList;
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import com.mongodb.BasicDBObject;
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import com.mongodb.DBCursor;
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import com.mongodb.DBObject;
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import org.broadinstitute.sting.commandline.*;
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import org.broadinstitute.sting.gatk.GenomeAnalysisEngine;
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import org.broadinstitute.sting.gatk.arguments.StandardVariantContextInputArgumentCollection;
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@ -40,12 +36,9 @@ import org.broadinstitute.sting.gatk.walkers.TreeReducible;
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import org.broadinstitute.sting.gatk.walkers.genotyper.GenotypeLikelihoodsCalculationModel;
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import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedArgumentCollection;
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import org.broadinstitute.sting.gatk.walkers.genotyper.UnifiedGenotyperEngine;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.MendelianViolation;
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import org.broadinstitute.sting.utils.SampleUtils;
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import org.broadinstitute.sting.utils.codecs.vcf.*;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.db.MongoDB;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import org.broadinstitute.sting.utils.text.XReadLines;
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import org.broadinstitute.sting.utils.variantcontext.*;
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@ -191,8 +184,7 @@ import java.util.*;
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*
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*/
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public class SelectVariants extends RodWalker<Integer, Integer> implements TreeReducible<Integer> {
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@ArgumentCollection
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protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
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@ArgumentCollection protected StandardVariantContextInputArgumentCollection variantCollection = new StandardVariantContextInputArgumentCollection();
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/**
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* A site is considered discordant if there exists some sample in the variant track that has a non-reference genotype
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@ -365,8 +357,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
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private Set<String> IDsToKeep = null;
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private final static boolean mongoOn = false;
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/**
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* Set up the VCF writer, the sample expressions and regexs, and the JEXL matcher
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*/
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@ -488,7 +478,7 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
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if ( tracker == null )
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return 0;
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Collection<VariantContext> vcs = mongoOn ? getMongoVariants(ref, context.getLocation()) : tracker.getValues(variantCollection.variants, context.getLocation());
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Collection<VariantContext> vcs = tracker.getValues(variantCollection.variants, context.getLocation());
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if ( vcs == null || vcs.size() == 0) {
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return 0;
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@ -568,193 +558,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
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return 1;
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}
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private Collection<VariantContext> getMongoVariants(ReferenceContext ref, GenomeLoc location) {
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String contig = location.getContig();
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long start = location.getStart();
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ArrayList<VariantContext> vcs = new ArrayList<VariantContext>();
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BasicDBObject query = new BasicDBObject();
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query.put("contig", contig);
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query.put("start", start);
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// can't know stop location for deletions from reference
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DBCursor attributesCursor = MongoDB.getAttributesCollection().find(query);
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DBCursor samplesCursor = MongoDB.getSamplesCollection().find(query);
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Map<Pair<String,List<Allele>>,VariantContextBuilder> attributesFromDB = new HashMap<Pair<String,List<Allele>>,VariantContextBuilder>();
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while(attributesCursor.hasNext()) {
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DBObject oneResult = attributesCursor.next();
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String sourceROD = (String)oneResult.get("sourceROD");
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ArrayList<Allele> alleles = new ArrayList<Allele>();
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BasicDBObject allelesInDb = (BasicDBObject)oneResult.get("alleles");
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for (Object alleleInDb : allelesInDb.values()) {
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String rawAllele = (String)alleleInDb;
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boolean isRef = rawAllele.contains("*");
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String allele = rawAllele.replace("*", "");
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alleles.add(Allele.create(allele, isRef));
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}
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// primary key to uniquely identify variant
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Pair<String, List<Allele>> sourceRodAllelePair = new Pair<String, List<Allele>>(sourceROD, alleles);
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Map<String, Object> attributes = new TreeMap<String, Object>();
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BasicDBList attrsInDb = (BasicDBList)oneResult.get("attributes");
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for (Object attrInDb : attrsInDb) {
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BasicDBObject attrKVP = (BasicDBObject)attrInDb;
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String key = (String)attrKVP.get("key");
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Object value = attrKVP.get("value");
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attributes.put(key, value);
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}
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Set<String> filters = new HashSet<String>();
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BasicDBObject filtersInDb = (BasicDBObject)oneResult.get("filters");
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if (filtersInDb != null) {
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for (Object filterInDb : filtersInDb.values()) {
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filters.add((String)filterInDb);
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}
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}
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String source = (String)oneResult.get("source");
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String id = (String)oneResult.get("id");
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Double error = (Double)oneResult.get("error");
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Long stop = (Long)oneResult.get("stop");
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VariantContextBuilder builder = new VariantContextBuilder(source, contig, start, stop, sourceRodAllelePair.getSecond());
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builder.id(id);
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builder.log10PError(error);
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builder.attributes(attributes);
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builder.filters(filters);
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long index = start - ref.getWindow().getStart() - 1;
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if ( index >= 0 ) {
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// we were given enough reference context to create the VariantContext
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builder.referenceBaseForIndel(ref.getBases()[(int)index]); // TODO: needed?
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}
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builder.referenceBaseForIndel(ref.getBases()[0]); // TODO: correct?
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attributesFromDB.put(sourceRodAllelePair, builder);
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}
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while(samplesCursor.hasNext()) {
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DBObject oneResult = samplesCursor.next();
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String sourceROD = (String)oneResult.get("sourceROD");
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ArrayList<Allele> alleles = new ArrayList<Allele>();
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BasicDBObject allelesInDb = (BasicDBObject)oneResult.get("alleles");
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for (Object alleleInDb : allelesInDb.values()) {
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String rawAllele = (String)alleleInDb;
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boolean isRef = rawAllele.contains("*");
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String allele = rawAllele.replace("*", "");
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alleles.add(Allele.create(allele, isRef));
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}
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// primary key to uniquely identify variant
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Pair<String, List<Allele>> sourceRodAllelePair = new Pair<String, List<Allele>>(sourceROD, alleles);
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VariantContextBuilder builder = attributesFromDB.get(sourceRodAllelePair);
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String sample = (String)oneResult.get("sample");
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BasicDBObject genotypeInDb = (BasicDBObject)oneResult.get("genotype");
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Double genotypeError = (Double)genotypeInDb.get("error");
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ArrayList<Allele> genotypeAlleles = new ArrayList<Allele>();
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BasicDBObject genotypeAllelesInDb = (BasicDBObject)genotypeInDb.get("alleles");
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for (Object alleleInDb : genotypeAllelesInDb.values()) {
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String rawAllele = (String)alleleInDb;
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boolean isRef = rawAllele.contains("*");
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String allele = rawAllele.replace("*", "");
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genotypeAlleles.add(Allele.create(allele, isRef));
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}
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Map<String, Object> genotypeAttributes = new TreeMap<String, Object>();
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BasicDBList genotypeAttrsInDb = (BasicDBList)genotypeInDb.get("attributes");
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for (Object attrInDb : genotypeAttrsInDb) {
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BasicDBObject attrKVP = (BasicDBObject)attrInDb;
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String key = (String)attrKVP.get("key");
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Object value = attrKVP.get("value");
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genotypeAttributes.put(key, value);
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}
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Genotype genotype = new Genotype(sample, genotypeAlleles, genotypeError);
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builder.genotypes(Genotype.modifyAttributes(genotype, genotypeAttributes));
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vcs.add(builder.make());
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}
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return combineMongoVariants(vcs);
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}
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// Copied from CombineVariants
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private Collection<VariantContext> combineMongoVariants(Collection<VariantContext> vcs) {
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if (vcs.size() < 2)
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return vcs;
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List<VariantContext> mergedVCs = new ArrayList<VariantContext>();
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//defaults from CombineVariants
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VariantContextUtils.MultipleAllelesMergeType multipleAllelesMergeType = VariantContextUtils.MultipleAllelesMergeType.BY_TYPE;
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List<String> priority = new ArrayList<String>();
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priority.add("input");
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VariantContextUtils.FilteredRecordMergeType filteredRecordsMergeType = VariantContextUtils.FilteredRecordMergeType.KEEP_IF_ANY_UNFILTERED;
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VariantContextUtils.GenotypeMergeType genotypeMergeOption = VariantContextUtils.GenotypeMergeType.PRIORITIZE;
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boolean printComplexMerges = false;
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String SET_KEY = "set";
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boolean filteredAreUncalled = false;
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boolean MERGE_INFO_WITH_MAX_AC = false;
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if (multipleAllelesMergeType == VariantContextUtils.MultipleAllelesMergeType.BY_TYPE) {
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Map<VariantContext.Type, List<VariantContext>> VCsByType = VariantContextUtils.separateVariantContextsByType(vcs);
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// TODO -- clean this up in a refactoring
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// merge NO_VARIATION into another type of variant (based on the ordering in VariantContext.Type)
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if ( VCsByType.containsKey(VariantContext.Type.NO_VARIATION) && VCsByType.size() > 1 ) {
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final List<VariantContext> refs = VCsByType.remove(VariantContext.Type.NO_VARIATION);
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for ( VariantContext.Type type : VariantContext.Type.values() ) {
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if ( VCsByType.containsKey(type) ) {
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VCsByType.get(type).addAll(refs);
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break;
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}
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}
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}
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// iterate over the types so that it's deterministic
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for (VariantContext.Type type : VariantContext.Type.values()) {
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if (VCsByType.containsKey(type))
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mergedVCs.add(VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(), VCsByType.get(type),
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priority, filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges,
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SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC));
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}
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}
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else if (multipleAllelesMergeType == VariantContextUtils.MultipleAllelesMergeType.MIX_TYPES) {
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mergedVCs.add(VariantContextUtils.simpleMerge(getToolkit().getGenomeLocParser(), vcs,
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priority, filteredRecordsMergeType, genotypeMergeOption, true, printComplexMerges,
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SET_KEY, filteredAreUncalled, MERGE_INFO_WITH_MAX_AC));
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}
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else {
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logger.warn("Ignoring all records at site");
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}
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List<VariantContext> recomputedVCs = new ArrayList<VariantContext>();
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for ( VariantContext mergedVC : mergedVCs ) {
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// only operate at the start of events
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if ( mergedVC == null )
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continue;
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final VariantContextBuilder builder = new VariantContextBuilder(mergedVC);
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// re-compute chromosome counts
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VariantContextUtils.calculateChromosomeCounts(builder, false);
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recomputedVCs.add(builder.make());
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}
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return recomputedVCs;
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}
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private boolean hasPLs(final VariantContext vc) {
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for ( Genotype g : vc.getGenotypes() ) {
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if ( g.hasLikelihoods() )
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@ -857,10 +660,6 @@ public class SelectVariants extends RodWalker<Integer, Integer> implements TreeR
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}
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public void onTraversalDone(Integer result) {
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if (mongoOn) {
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MongoDB.close();
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}
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logger.info(result + " records processed.");
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if (SELECT_RANDOM_NUMBER) {
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@ -1,52 +0,0 @@
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package org.broadinstitute.sting.utils.db;
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import com.mongodb.DB;
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import com.mongodb.DBCollection;
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import com.mongodb.Mongo;
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import org.broadinstitute.sting.utils.exceptions.StingException;
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import java.net.UnknownHostException;
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/**
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* Created with IntelliJ IDEA.
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* User: thibault
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* Date: 4/26/12
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* Time: 3:01 PM
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* Handles Mongo DB connections
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*/
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final public class MongoDB {
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private final static String MONGO_HOST = "couchdb.broadinstitute.org";
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private final static Integer MONGO_PORT = 43054;
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private final static String MONGO_DB_NAME = "bjorn";
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private final static String MONGO_ATTRIBUTES_COLLECTION = "attributes";
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private final static String MONGO_SAMPLES_COLLECTION = "samples";
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protected Mongo mongo;
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protected DBCollection mongoAttributes;
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protected DBCollection mongoSamples;
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final private static MongoDB INSTANCE = new MongoDB();
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public static DBCollection getAttributesCollection() {
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return INSTANCE.mongoAttributes;
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}
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public static DBCollection getSamplesCollection() {
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return INSTANCE.mongoSamples;
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}
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public static void close() {
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INSTANCE.mongo.close();
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}
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private MongoDB() {
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try {
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mongo = new Mongo(MONGO_HOST, MONGO_PORT);
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DB mongoDb = mongo.getDB(MONGO_DB_NAME);
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mongoAttributes = mongoDb.getCollection(MONGO_ATTRIBUTES_COLLECTION);
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mongoSamples = mongoDb.getCollection(MONGO_SAMPLES_COLLECTION);
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} catch (UnknownHostException e) {
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throw new StingException(e.getMessage(), e);
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}
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}
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}
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@ -1,11 +1,9 @@
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package org.broadinstitute.sting.utils.variantcontext;
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import com.mongodb.BasicDBObject;
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import org.broad.tribble.Feature;
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import org.broad.tribble.TribbleException;
|
||||
import org.broad.tribble.util.ParsingUtils;
|
||||
import org.broadinstitute.sting.utils.codecs.vcf.VCFConstants;
|
||||
import org.broadinstitute.sting.utils.collections.Pair;
|
||||
import org.broadinstitute.sting.utils.exceptions.ReviewedStingException;
|
||||
|
||||
import java.util.*;
|
||||
|
|
@ -1220,101 +1218,6 @@ public class VariantContext implements Feature { // to enable tribble integratio
|
|||
this.getGenotypes());
|
||||
}
|
||||
|
||||
/**
|
||||
* Generate a Mongo DB attributes collection element and a set of samples collection elements
|
||||
* @param sourceROD
|
||||
* @return
|
||||
*/
|
||||
public Pair<BasicDBObject,List<BasicDBObject>> toMongoDB(String sourceROD) {
|
||||
// fields common to both attributes and samples collections
|
||||
BasicDBObject siteDoc = new BasicDBObject();
|
||||
|
||||
siteDoc.put("location", contig + ":" + (start - stop == 0 ? start : start + "-" + stop));
|
||||
siteDoc.put("contig", contig);
|
||||
siteDoc.put("start", start);
|
||||
siteDoc.put("stop", stop);
|
||||
siteDoc.put("id", this.getID());
|
||||
siteDoc.put("error", this.getLog10PError());
|
||||
siteDoc.put("source", this.getSource());
|
||||
siteDoc.put("sourceROD", sourceROD);
|
||||
siteDoc.put("type", this.getType().toString());
|
||||
|
||||
Integer alleleIndex = 0;
|
||||
BasicDBObject allelesDoc = new BasicDBObject();
|
||||
for (Allele allele : this.getAlleles())
|
||||
{
|
||||
String index = alleleIndex.toString();
|
||||
allelesDoc.put(index, allele.toString());
|
||||
alleleIndex++;
|
||||
}
|
||||
siteDoc.put("alleles", allelesDoc);
|
||||
|
||||
Integer filterIndex = 0;
|
||||
BasicDBObject filtersDoc = new BasicDBObject();
|
||||
for (String filter : this.getFilters())
|
||||
{
|
||||
String index = filterIndex.toString();
|
||||
filtersDoc.put(index, filter.toString());
|
||||
filterIndex++;
|
||||
}
|
||||
if (filterIndex > 0) {
|
||||
siteDoc.put("filters", filtersDoc);
|
||||
}
|
||||
|
||||
// attributes collection
|
||||
|
||||
BasicDBObject attributesDoc = new BasicDBObject(siteDoc);
|
||||
List<BasicDBObject> attributeKVPs = new ArrayList<BasicDBObject>();
|
||||
for (Map.Entry<String, Object> attribute : this.getAttributes().entrySet() )
|
||||
{
|
||||
String key = attribute.getKey();
|
||||
Object value = attribute.getValue();
|
||||
BasicDBObject attributeKVP = new BasicDBObject();
|
||||
attributeKVP.put("key", key);
|
||||
attributeKVP.put("value", value);
|
||||
attributeKVPs.add(attributeKVP);
|
||||
}
|
||||
attributesDoc.put("attributes", attributeKVPs);
|
||||
|
||||
// samples collection
|
||||
|
||||
List<BasicDBObject> samplesDocs = new ArrayList<BasicDBObject>();
|
||||
for (Genotype genotype : this.getGenotypes()) {
|
||||
BasicDBObject sampleDoc = new BasicDBObject(siteDoc);
|
||||
sampleDoc.put("sample", genotype.getSampleName());
|
||||
|
||||
BasicDBObject genotypesDoc = new BasicDBObject();
|
||||
Integer genotypeAlleleIndex = 0;
|
||||
BasicDBObject genotypeAllelesDoc = new BasicDBObject();
|
||||
for (Allele allele : genotype.getAlleles())
|
||||
{
|
||||
String index = genotypeAlleleIndex.toString();
|
||||
genotypeAllelesDoc.put(index, allele.toString());
|
||||
genotypeAlleleIndex++;
|
||||
}
|
||||
genotypesDoc.put("alleles", genotypeAllelesDoc);
|
||||
|
||||
List<BasicDBObject> genotypesAttributesDocs = new ArrayList<BasicDBObject>();
|
||||
for (Map.Entry<String, Object> attribute : genotype.getAttributes().entrySet() )
|
||||
{
|
||||
String key = attribute.getKey();
|
||||
Object value = attribute.getValue();
|
||||
BasicDBObject genotypesAttributesDoc = new BasicDBObject();
|
||||
genotypesAttributesDoc.put("key", key);
|
||||
genotypesAttributesDoc.put("value", value);
|
||||
genotypesAttributesDocs.add(genotypesAttributesDoc);
|
||||
}
|
||||
genotypesDoc.put("attributes", genotypesAttributesDocs);
|
||||
genotypesDoc.put("error", genotype.getLog10PError());
|
||||
|
||||
sampleDoc.put("genotype", genotypesDoc);
|
||||
|
||||
samplesDocs.add(sampleDoc);
|
||||
}
|
||||
|
||||
return new Pair<BasicDBObject,List<BasicDBObject>>(attributesDoc, samplesDocs);
|
||||
}
|
||||
|
||||
// protected basic manipulation routines
|
||||
private static List<Allele> makeAlleles(Collection<Allele> alleles) {
|
||||
final List<Allele> alleleList = new ArrayList<Allele>(alleles.size());
|
||||
|
|
|
|||
Loading…
Reference in New Issue