Transitioned over to VE3 architecture.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5141 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
kiran
parent
401feca90d
commit
3f387bc8d8
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@ -6,7 +6,7 @@ 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.gatk.walkers.varianteval.VariantEvalWalker;
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import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvaluator;
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import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
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import org.broadinstitute.sting.utils.collections.Pair;
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import org.broadinstitute.sting.utils.report.tags.Analysis;
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import org.broadinstitute.sting.utils.report.tags.DataPoint;
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@ -56,7 +56,7 @@ public class ACTransitionTable extends VariantEvaluator {
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public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( eval != null && ! initialized ) {
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this.veWalker.getLogger().warn("Initializing...");
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//this.veWalker.getLogger().warn("Initializing...");
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initialize(eval);
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initialized = true;
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}
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@ -112,13 +112,13 @@ public class ACTransitionTable extends VariantEvaluator {
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}
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public ACTransitionTable(VariantEvalWalker parent) {
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super(parent);
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//super(parent);
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}
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public void initialize(VariantContext vc) {
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Set<String> permuteSamples = vc.getSampleNames();
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permutations = new String[NUM_PERMUTATIONS][permuteSamples.size()];
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veWalker.getLogger().warn(String.format("Num samples: %d",permuteSamples.size()));
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//veWalker.getLogger().warn(String.format("Num samples: %d",permuteSamples.size()));
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int offset = 0;
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for ( String s : permuteSamples ) {
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permutations[0][offset] = s;
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@ -145,7 +145,7 @@ public class ACTransitionTable extends VariantEvaluator {
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}
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public void finalizeEvaluation() { // note: data points are null when this is called (wtf?)
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veWalker.getLogger().info(String.format("Skipped: %d",skipped));
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//veWalker.getLogger().info(String.format("Skipped: %d",skipped));
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}
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class TransitionTable implements TableType {
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@ -6,9 +6,9 @@ import org.broadinstitute.sting.gatk.contexts.ReferenceContext;
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import org.broadinstitute.sting.gatk.contexts.variantcontext.VariantContextUtils;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
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import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvaluator;
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import org.broadinstitute.sting.utils.report.tags.Analysis;
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import org.broadinstitute.sting.utils.report.tags.DataPoint;
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import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
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import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
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import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
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import org.broadinstitute.sting.utils.report.utils.TableType;
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import org.broadinstitute.sting.utils.analysis.AminoAcid;
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import org.broadinstitute.sting.utils.analysis.AminoAcidTable;
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@ -53,7 +53,7 @@ public class AminoAcidTransition extends VariantEvaluator {
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////////////////////////////////////////////////////////////
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// a mapping from amino acid transition score histogram bin to Ti/Tv ratio
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@DataPoint(name="Amino Acid Table", description = "TiTv counts by amino acid change")
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@DataPoint(description = "TiTv counts by amino acid change")
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AminoAcidTiTvTable acidTable = null;
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class TiTvCount {
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@ -129,8 +129,9 @@ public class AminoAcidTransition extends VariantEvaluator {
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private AminoAcidTable lookup;
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public AminoAcidTransition(VariantEvalWalker parent) {
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super(parent);
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enabled = parent.aminoAcidTransitionKey != null;
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//super(parent);
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//enabled = parent.aminoAcidTransitionKey != null;
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enabled = true;
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if ( enabled ) {
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getParsingInformation(parent);
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lookup = new AminoAcidTable();
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@ -140,9 +141,14 @@ public class AminoAcidTransition extends VariantEvaluator {
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private void getParsingInformation(VariantEvalWalker parent) {
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if ( enabled() ) {
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infoKey = parent.aminoAcidTransitionKey;
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infoValueSplit = parent.aminoAcidTransitionSplit;
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useCodons = parent.aatUseCodons;
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// infoKey = parent.aminoAcidTransitionKey;
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// infoValueSplit = parent.aminoAcidTransitionSplit;
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// useCodons = parent.aatUseCodons;
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infoKey = null;
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infoValueSplit = null;
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useCodons = false;
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if ( infoKey == null ) {
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throw new UserException.CommandLineException("No info-field key provided for amino acid tabulation. Please provide the appropriate key with -aatk.");
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}
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@ -180,7 +186,7 @@ public class AminoAcidTransition extends VariantEvaluator {
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first = parsedNames [0];
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second = parsedNames [1];
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} catch (ArrayIndexOutOfBoundsException e) {
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getLogger().warn("Error parsing variant context with value "+eval.getAttribute(infoKey));
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//getLogger().warn("Error parsing variant context with value "+eval.getAttribute(infoKey));
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}
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AminoAcid reference;
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AminoAcid alternate;
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@ -1,75 +0,0 @@
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package org.broadinstitute.sting.oneoffprojects.walkers.varianteval;
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import org.broad.tribble.util.variantcontext.Genotype;
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import org.broad.tribble.util.variantcontext.VariantContext;
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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.gatk.walkers.varianteval.VariantEvalWalker;
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import org.broadinstitute.sting.utils.report.tags.Analysis;
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import java.util.ArrayList;
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import java.util.List;
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/**
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* Extends the Per-sample variant evaluator class and returns, for each sample, the number of variants, the Ti/Tv, and
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* the comp overlap. It does this only on sites where the sample is identified as hom var, or het.
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*/
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@org.broadinstitute.sting.utils.report.tags.Analysis(name="FunctionalClassBySample",description="Count of SNPs by functional class by sample")
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public class FunctionalClassBySample extends VariantEvaluatorBySample {
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public FunctionalClassBySample(VariantEvalWalker parent) { super(parent); }
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public List<SampleDataPoint> getDataPoints() {
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List<SampleDataPoint> points = new ArrayList<SampleDataPoint>(10);
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points.add(new FCPoint("miRNA","miRNA"));
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points.add(new FCPoint("3'-UTR","3'-UTR"));
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points.add(new FCPoint("Intron","Intron"));
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points.add(new FCPoint("Splice_site","Splice_site"));
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points.add(new FCPoint("Read-through","Read-through"));
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points.add(new FCPoint("Nonsense","Nonsense"));
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points.add(new FCPoint("Missense","Missense"));
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points.add(new FCPoint("Synonymous","Synonymous"));
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points.add(new FCPoint("5'-UTR","5'-UTR"));
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points.add(new FCPoint("Promoter","Promoter"));
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return points;
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}
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public String getTableName() { return "Functional Class Counts by Sample"; }
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public String getName() { return "Functional Class Counts by Sample"; }
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public int getComparisonOrder() { return 1; }
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public boolean enabled() { return true; }
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public boolean includeGenotype(Genotype g) { return ( ! g.isFiltered() ) && ( g.isHet() || g.isHomVar() ); }
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}
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class FCPoint extends SampleDataPoint {
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private String matchStr;
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private int count;
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public FCPoint(String fcName, String fcMatch) {
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super(fcName);
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matchStr = fcMatch;
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count = 0;
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}
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public void update1(VariantContext vc, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( vc == null ) {
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return;
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} else {
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String type = vc.getAttributeAsString("type","none");
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if ( type.equalsIgnoreCase(matchStr) ) {
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count++;
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}
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}
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}
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public String toString() {
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return String.format("%d",count);
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}
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}
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@ -6,9 +6,9 @@ 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.gatk.walkers.varianteval.VariantEvalWalker;
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import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvaluator;
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import org.broadinstitute.sting.utils.report.tags.Analysis;
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import org.broadinstitute.sting.utils.report.tags.DataPoint;
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import org.broadinstitute.sting.gatk.walkers.varianteval.evaluators.VariantEvaluator;
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import org.broadinstitute.sting.gatk.walkers.varianteval.tags.Analysis;
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import org.broadinstitute.sting.gatk.walkers.varianteval.tags.DataPoint;
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import org.broadinstitute.sting.utils.report.utils.TableType;
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import java.util.Arrays;
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@ -31,7 +31,7 @@ public class PrivatePermutations extends VariantEvaluator {
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private boolean initialized = false;
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private long skipped = 0l;
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@DataPoint(name="Marginal Number of Mutations",description="Number of additional mutations from each new sample; random permutations")
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@DataPoint(description="Number of additional mutations from each new sample; random permutations")
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AdditionalBySample permuteCounts = null;
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String[][] permutations;
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@ -50,7 +50,7 @@ public class PrivatePermutations extends VariantEvaluator {
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public String update2(VariantContext eval, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( eval != null && ! initialized ) {
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this.veWalker.getLogger().warn("Initializing...");
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//this.veWalker.getLogger().warn("Initializing...");
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initialize(eval);
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initialized = true;
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}
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@ -100,13 +100,13 @@ public class PrivatePermutations extends VariantEvaluator {
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}
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public PrivatePermutations(VariantEvalWalker parent) {
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super(parent);
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//super(parent);
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}
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public void initialize(VariantContext vc) {
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Set<String> permuteSamples = vc.getSampleNames();
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permutations = new String[NUM_PERMUTATIONS][permuteSamples.size()];
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veWalker.getLogger().warn(String.format("Num samples: %d",permuteSamples.size()));
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//veWalker.getLogger().warn(String.format("Num samples: %d",permuteSamples.size()));
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int offset = 0;
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for ( String s : permuteSamples ) {
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permutations[0][offset] = s;
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@ -164,6 +164,6 @@ public class PrivatePermutations extends VariantEvaluator {
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}
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public void finalizeEvaluation() {
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veWalker.getLogger().info(String.format("Skipped: %d",skipped));
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//veWalker.getLogger().info(String.format("Skipped: %d",skipped));
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}
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}
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@ -1,138 +0,0 @@
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package org.broadinstitute.sting.oneoffprojects.walkers.varianteval;
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import org.broad.tribble.util.variantcontext.Genotype;
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import org.broad.tribble.util.variantcontext.VariantContext;
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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.contexts.variantcontext.VariantContextUtils;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvalWalker;
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import org.broadinstitute.sting.utils.report.tags.Analysis;
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import java.util.ArrayList;
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import java.util.List;
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/**
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* Extends the Per-sample variant evaluator class and returns, for each sample, the number of variants, the Ti/Tv, and
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* the comp overlap. It does this only on sites where the sample is identified as hom var, or het.
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*/
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@Analysis(name = "Simple Metrics by Sample", description = "Variant counts, Ti/Tv, comp overlap; per sample")
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public class SimpleMetricsBySample extends VariantEvaluatorBySample {
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public SimpleMetricsBySample(VariantEvalWalker parent) { super(parent); }
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public List<SampleDataPoint> getDataPoints() {
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List<SampleDataPoint> points = new ArrayList(3);
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points.add(new CountSNPsSample());
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points.add(new TiTvRatioSample());
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points.add(new HetHomRatioSample());
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points.add(new CompOverlapSample());
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return points;
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}
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public String getTableName() {
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return "SimpleMetricsBySample";
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}
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public String getName() {
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return "SimpleMetricsBySample";
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}
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public int getComparisonOrder() { return 2; }
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public boolean includeGenotype(Genotype g) {
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return (g.isHet() || g.isHomVar()) && ! g.isFiltered();
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}
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public boolean enabled() {
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return true;
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}
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}
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class CountSNPsSample extends SampleDataPoint {
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int numVariants = 0;
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public CountSNPsSample() {
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super("CountVariants");
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}
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public void update2(VariantContext vc, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( vc != null && vc.isSNP() ) {
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numVariants++;
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}
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}
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public String toString() {
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return String.format("%d",numVariants);
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}
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}
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class TiTvRatioSample extends SampleDataPoint {
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int nTi = 0;
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int nTv = 0;
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public TiTvRatioSample() {
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super("TiTvRatio");
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}
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public void update2(VariantContext vc, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( vc != null && vc.isSNP() && vc.isBiallelic() ) {
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if ( VariantContextUtils.isTransition(vc) ) {
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nTi++;
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} else {
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nTv++;
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}
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}
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}
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public String toString() {
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return String.format("%.2f", ( ((double) nTi )/ nTv));
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}
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}
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class HetHomRatioSample extends SampleDataPoint {
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int nHet = 0;
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int nHomVar = 0;
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public HetHomRatioSample() {
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super("HetHomRatio");
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}
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public void update2(VariantContext vc, VariantContext comp, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( vc != null ) {
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Genotype g = vc.getGenotype(sampleName);
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if ( g != null ) {
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if ( g.isHet() ) {
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nHet++;
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} else if (g.isHomVar()) {
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nHomVar++;
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}
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}
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}
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}
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public String toString() {
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return String.format("%.2f", ( ((double) nHet )/ nHomVar));
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}
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}
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class CompOverlapSample extends SampleDataPoint {
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int nOverlap = 0;
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public CompOverlapSample() {
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super("CompOverlap");
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}
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public void update2(VariantContext eval, VariantContext comp,RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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boolean compIsGood = comp != null && comp.isNotFiltered() && comp.isSNP() ;
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boolean evalIsGood = eval != null && eval.isSNP();
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if ( compIsGood && evalIsGood ) {
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nOverlap++;
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}
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}
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public String toString() {
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return String.format("%d",nOverlap);
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}
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}
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@ -1,200 +0,0 @@
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package org.broadinstitute.sting.oneoffprojects.walkers.varianteval;
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import org.broad.tribble.util.variantcontext.Genotype;
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import org.broad.tribble.util.variantcontext.VariantContext;
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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.gatk.walkers.varianteval.VariantEvalWalker;
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import org.broadinstitute.sting.gatk.walkers.varianteval.VariantEvaluator;
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import org.broadinstitute.sting.utils.report.tags.DataPoint;
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import org.broadinstitute.sting.utils.report.utils.TableType;
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import java.util.*;
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/**
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* An abstract way to break variant analyses down by sample. SampleDataPoint objects (e.g. its inheritors) are propagated
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* into a per-sample table, which is updated only when a specific sample's genotype is such that the module-defined
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* includeGenotype(G) returns true.
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* @Author chartl
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*/
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public abstract class VariantEvaluatorBySample extends VariantEvaluator {
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@DataPoint(name="VariantEvaluatorBySample",description="Evaluation broken down by sample")
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EvalBySample evalBySample;
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public VariantEvaluatorBySample(VariantEvalWalker parent) {
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super(parent);
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evalBySample = initializeTable();
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}
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public abstract String getTableName();
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public abstract List<SampleDataPoint> getDataPoints();
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public abstract boolean includeGenotype(Genotype g);
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public EvalBySample initializeTable() {
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if ( enabled() ) {
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EvalBySample ebs = new EvalBySample(getTableName(),getDataPoints());
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return ebs;
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} else {
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return null;
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}
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}
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// note -- this only updates at all sites after the first site where a sample has been identified containing a variant genotype
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||||
public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
|
||||
for ( Map.Entry<String,List<SampleDataPoint>> entry : evalBySample.sampleAndEvalResults.entrySet() ) {
|
||||
for ( SampleDataPoint dp : entry.getValue() ) {
|
||||
dp.update0(tracker,ref,context);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
public String update1(VariantContext vc1, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
|
||||
for ( String sample : vc1.getSampleNames() ) {
|
||||
if ( includeGenotype(vc1.getGenotype(sample)) ) {
|
||||
if ( ! evalBySample.containsKey(sample) ) {
|
||||
evalBySample.put(sample,getDataPoints());
|
||||
}
|
||||
|
||||
for ( SampleDataPoint dp : evalBySample.sampleAndEvalResults.get(sample) ) {
|
||||
dp.update1(vc1,tracker,ref,context);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return null; // don't return interesting sites
|
||||
}
|
||||
|
||||
public String update2(VariantContext vc1, VariantContext vc2, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
|
||||
if ( vc1 == null ) {
|
||||
return null; // cannot update by sample if there are no samples
|
||||
}
|
||||
for ( String sample : vc1.getSampleNames() ) {
|
||||
if ( includeGenotype(vc1.getGenotype(sample)) ) {
|
||||
if ( ! evalBySample.containsKey(sample) ) {
|
||||
evalBySample.put(sample,getDataPoints());
|
||||
}
|
||||
|
||||
for ( SampleDataPoint dp : evalBySample.sampleAndEvalResults.get(sample) ) {
|
||||
dp.update2(vc1,vc2,tracker,ref,context);
|
||||
}
|
||||
}
|
||||
}
|
||||
|
||||
return null; // don't return interesting sites
|
||||
}
|
||||
|
||||
@Override
|
||||
public void finalizeEvaluation() {
|
||||
evalBySample.finalizeTable();
|
||||
}
|
||||
|
||||
}
|
||||
|
||||
abstract class SampleDataPoint {
|
||||
public String name;
|
||||
public String sampleName;
|
||||
|
||||
public SampleDataPoint(String name) {
|
||||
this.name = name;
|
||||
}
|
||||
|
||||
public String getName() {
|
||||
return name;
|
||||
}
|
||||
|
||||
public void setSampleName(String sName) {
|
||||
sampleName = sName;
|
||||
}
|
||||
|
||||
public abstract String toString();
|
||||
|
||||
public void update0(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {}
|
||||
|
||||
public void update1(VariantContext vc, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {}
|
||||
|
||||
public void update2(VariantContext eval, VariantContext comp,RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {}
|
||||
|
||||
public void finalizeCalculation() {}
|
||||
}
|
||||
|
||||
class EvalBySample implements TableType {
|
||||
public String[] evalNames;
|
||||
public TreeMap<String, List<SampleDataPoint>> sampleAndEvalResults;
|
||||
public String name;
|
||||
private HashMap<String,Integer> nameToDataPointOffset;
|
||||
|
||||
private Object[][] finalizedResults;
|
||||
|
||||
public EvalBySample(String name, Collection<SampleDataPoint> evals) {
|
||||
int i = 0;
|
||||
this.evalNames = new String[evals.size()];
|
||||
this.nameToDataPointOffset = new HashMap<String,Integer>(evals.size());
|
||||
for ( SampleDataPoint s : evals ) {
|
||||
this.evalNames[i] = s.getName();
|
||||
this.nameToDataPointOffset.put(s.getName(),i);
|
||||
i++;
|
||||
}
|
||||
|
||||
this.name = name;
|
||||
this.sampleAndEvalResults = new TreeMap<String,List<SampleDataPoint>>();
|
||||
}
|
||||
|
||||
public Object[] getColumnKeys() {
|
||||
//System.out.printf("%s%n","Call to column keys");
|
||||
return evalNames;
|
||||
}
|
||||
|
||||
public String getCell(int x, int y) {
|
||||
return finalizedResults[x][y].toString();
|
||||
}
|
||||
|
||||
public String getName() {
|
||||
return name;
|
||||
}
|
||||
|
||||
public Object[] getRowKeys() {
|
||||
String[] rowNames = new String[sampleAndEvalResults.size()];
|
||||
int i = 0;
|
||||
for ( Map.Entry<String,List<SampleDataPoint>> e : sampleAndEvalResults.entrySet() ) {
|
||||
rowNames[i] = e.getKey();
|
||||
i++;
|
||||
}
|
||||
|
||||
//System.out.printf("%s%n","Call to row keys");
|
||||
|
||||
return rowNames;
|
||||
}
|
||||
|
||||
public void finalizeTable() {
|
||||
if ( sampleAndEvalResults == null || sampleAndEvalResults.size() == 0 ) {
|
||||
finalizedResults = new Object[0][0];
|
||||
return; // todo -- early return is hacky
|
||||
}
|
||||
finalizedResults = new Object[sampleAndEvalResults.size()][sampleAndEvalResults.firstEntry().getValue().size()];
|
||||
int i = 0;
|
||||
for ( Map.Entry<String,List<SampleDataPoint>> evalBySample : sampleAndEvalResults.entrySet() ) {
|
||||
int j = 0;
|
||||
for ( SampleDataPoint o : evalBySample.getValue() ) {
|
||||
o.finalizeCalculation();
|
||||
finalizedResults[i][j] = o;
|
||||
j++;
|
||||
}
|
||||
i++;
|
||||
}
|
||||
}
|
||||
|
||||
public boolean containsKey(String sample) {
|
||||
return sampleAndEvalResults.containsKey(sample);
|
||||
}
|
||||
|
||||
public void put(String sample, List<SampleDataPoint> dataPoints) {
|
||||
for ( SampleDataPoint dp : dataPoints ) {
|
||||
dp.setSampleName(sample);
|
||||
}
|
||||
sampleAndEvalResults.put(sample,dataPoints);
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue