Name and body change for this module to reflect local code.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3675 348d0f76-0448-11de-a6fe-93d51630548a
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chartl
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package org.broadinstitute.sting.oneoffprojects.walkers.varianteval;
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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.VariantContext;
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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.playground.utils.report.tags.Analysis;
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import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
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import org.broadinstitute.sting.playground.utils.report.utils.TableType;
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import org.broadinstitute.sting.utils.StingException;
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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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import org.broadinstitute.sting.utils.analysis.AminoAcidUtils;
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import java.util.ArrayList;
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/*
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* Copyright (c) 2010 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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/**
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* @author chartl
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* @since June 28, 2010
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*/
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@Analysis(name = "Amino Acid Transition", description = "Calculates the Transition Matrix for coding variants; entries are Total, Num. Ti, Num. Tv, Ratio")
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public class AminoAcidTransition extends VariantEvaluator {
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////////////////////////////////////////////////////////////
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//// INTERNAL DATA POINT CLASSES
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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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AminoAcidTiTvTable acidTable = null;
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class TiTvCount {
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public int ti;
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public int tv;
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public TiTvCount() {
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ti = 0;
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tv = 0;
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}
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public int getTotal() {
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return ti + tv;
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}
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public double getRatio() {
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return ( (double) ti )/tv;
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}
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public String toString() {
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return String.format("%d:%d:%d:%f",getTotal(),ti,tv,getRatio());
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}
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}
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class AminoAcidTiTvTable implements TableType {
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private TiTvCount[][] countsByAAChange;
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public AminoAcidTiTvTable() {
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countsByAAChange = new TiTvCount[AminoAcid.values().length][AminoAcid.values().length];
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for ( int i = 0; i < AminoAcid.values().length; i ++ ) {
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for ( int j = 0; j < AminoAcid.values().length; j++ ) {
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countsByAAChange[i][j] = new TiTvCount();
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}
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}
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}
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public Object[] getRowKeys() {
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return AminoAcidUtils.getAminoAcidCodes();
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}
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public Object[] getColumnKeys() {
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return AminoAcidUtils.getAminoAcidCodes();
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}
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public TiTvCount getCell(int x, int y) {
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return countsByAAChange[x][y];
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}
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public String getName() {
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return "AminoAcidTransitionTable";
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}
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public void update(AminoAcid reference, AminoAcid alternate, boolean isTransition) {
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TiTvCount counter = countsByAAChange[reference.ordinal()][alternate.ordinal()];
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if ( isTransition ) {
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counter.ti++;
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} else {
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counter.tv++;
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}
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}
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}
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////////////////////////////////////////////////////////////
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//// CORE VARIANT EVALUATOR DATA AND METHODS
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////////////////////////////////////////////////////////////
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private String infoKey;
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private String infoValueSplit;
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private boolean useCodons;
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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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getParsingInformation(parent);
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lookup = new AminoAcidTable();
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}
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private void getParsingInformation(VariantEvalWalker parent) {
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// todo -- allow me to be flexible
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infoKey = "something";
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infoValueSplit = "somethingElse";
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useCodons = false;
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}
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public String getName() {
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return "AminoAcidTransitionTable";
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}
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public int getComparisonOrder() {
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return 1; // we only need to see each eval track
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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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public String toString() {
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return getName();
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}
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public String update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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String interesting = null;
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if ( eval != null && eval.hasAttribute(infoKey) ) {
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String[] parsedNames = ( (String) eval.getAttribute(infoKey)).split(infoValueSplit);
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String first = parsedNames [0];
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String second = parsedNames [1];
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AminoAcid reference;
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AminoAcid alternate;
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if ( useCodons ) {
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reference = lookup.getEukaryoticAA(first);
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alternate = lookup.getEukaryoticAA(second);
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} else {
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reference = lookup.getAminoAcidByCode(first);
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alternate = lookup.getAminoAcidByCode(second);
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}
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if ( reference == null ) {
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interesting = "Unknown Reference Codon";
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} else if ( alternate == null ) {
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interesting = "Unknown Alternate Codon";
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} else {
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acidTable.update(reference,alternate,eval.isTransition());
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}
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}
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return interesting; // This module doesn't capture any interesting sites, so return null
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}
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//public void finalizeEvaluation() {
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//
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//}
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}
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@ -1,178 +0,0 @@
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package org.broadinstitute.sting.oneoffprojects.walkers.varianteval;
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/*
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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.VariantContext;
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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.playground.utils.report.tags.Analysis;
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import org.broadinstitute.sting.playground.utils.report.tags.DataPoint;
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import org.broadinstitute.sting.playground.utils.report.utils.TableType;
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import org.broadinstitute.sting.utils.StingException;
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import java.util.ArrayList;
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/*
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* Copyright (c) 2010 The Broad Institute
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*
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* Permission is hereby granted, free of charge, to any person
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* obtaining a copy of this software and associated documentation
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* files (the "Software"), to deal in the Software without
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* restriction, including without limitation the rights to use,
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* copy, modify, merge, publish, distribute, sublicense, and/or sell
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* copies of the Software, and to permit persons to whom the
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* Software is furnished to do so, subject to the following
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* conditions:
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*
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* The above copyright notice and this permission notice shall be
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* included in all copies or substantial portions of the Software.
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*
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* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
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* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
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* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
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* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
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* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
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* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
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* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
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* OTHER DEALINGS IN THE SOFTWARE.
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*/
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/**
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* @author depristo
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* @since Apr 11, 2010
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*/
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/*
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@Analysis(name = "BLOSUM Matrix", description = "Calculates the BLOSUM Matrix for coding variants")
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public class BLOSUMMatrix extends VariantEvaluator {
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// a mapping from quality score histogram bin to Ti/Tv ratio
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@DataPoint(name="TiTv by AC", description = "TiTv by allele count")
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MetricsByAc metrics = null;
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//@DataPoint(name="Quality by Allele Count", description = "average variant quality for each allele count")
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//AlleleCountStats alleleCountStats = null;
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private final static Object[] METRIC_COLUMNS = {"AC", "nTi", "nTv", "n", "Ti/Tv"};
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class MetricsAtAC {
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public int ac = -1, nTi = 0, nTv = 0;
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public MetricsAtAC(int ac) { this.ac = ac; }
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public void update(VariantContext eval) {
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if ( eval.isTransition() )
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nTi++;
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else
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nTv++;
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}
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// corresponding to METRIC_COLUMNS
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public String getColumn(int i) {
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switch (i) {
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case 0: return String.valueOf(ac);
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case 1: return String.valueOf(nTi);
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case 2: return String.valueOf(nTv);
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case 3: return String.valueOf(nTi + nTv);
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case 4: return String.valueOf(ratio(nTi, nTv));
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default:
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throw new StingException("Unexpected column " + i);
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}
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}
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}
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class MetricsByAc implements TableType {
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ArrayList<MetricsAtAC> metrics = new ArrayList<MetricsAtAC>();
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Object[] rows = null;
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public MetricsByAc( int nchromosomes ) {
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rows = new Object[nchromosomes+1];
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metrics = new ArrayList<MetricsAtAC>(nchromosomes+1);
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for ( int i = 0; i < nchromosomes + 1; i++ ) {
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metrics.add(new MetricsAtAC(i));
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rows[i] = "ac" + i;
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}
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}
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public Object[] getRowKeys() {
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return rows;
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}
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public Object[] getColumnKeys() {
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return METRIC_COLUMNS;
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}
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public String getName() {
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return "MetricsByAc";
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}
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//
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public String getCell(int ac, int y) {
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return metrics.get(ac).getColumn(y);
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}
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public String toString() {
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String returnString = "";
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return returnString;
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}
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public void incrValue( VariantContext eval ) {
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int ac = -1;
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if ( eval.hasGenotypes() )
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ac = eval.getChromosomeCount(eval.getAlternateAllele(0));
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else if ( eval.hasAttribute("AC") ) {
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ac = Integer.valueOf(eval.getAttributeAsString("AC"));
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}
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if ( ac != -1 )
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metrics.get(ac).update(eval);
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}
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}
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public BLOSUMMatrix(VariantEvalWalker parent) {
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super(parent);
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// don't do anything
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}
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public String getName() {
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return "SimpleMetricsByAC";
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}
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public int getComparisonOrder() {
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return 1; // we only need to see each eval track
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}
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public boolean enabled() {
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return false;
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}
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public String toString() {
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return getName();
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}
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public String update1(VariantContext eval, RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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final String interesting = null;
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if (eval != null ) {
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if ( metrics == null ) {
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int nSamples = this.getVEWalker().getNSamplesForEval(eval);
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if ( nSamples != -1 )
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metrics = new MetricsByAc(2 * nSamples);
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}
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if ( eval.isSNP() &&
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eval.isBiallelic() &&
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metrics != null ) {
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metrics.incrValue(eval);
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}
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}
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return interesting; // This module doesn't capture any interesting sites, so return null
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}
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//public void finalizeEvaluation() {
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//
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//}
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}*/
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