Initial commit of items for analyzing amino acid transitions in variant eval. Blew up my subversion by coding locally while i did not have internet. I hope this doesn't bust any integrationtests since I changed no existing code but...who knows. Crossing my fingers.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3672 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
chartl
parent
e3fb4d5c70
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3017f82550
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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 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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@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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@ -0,0 +1,89 @@
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package org.broadinstitute.sting.utils.analysis;
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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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public enum AminoAcid {
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Alanine("Alanine","Ala","A",new String[]{"GCA","GCC","GCG","GCT"}),
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Arganine("Arganine","Arg","R",new String[]{"AGA","AGG","CGA","CGC","CGG","CGT"}),
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Asparagine("Asparagine","Asn","N",new String[]{"AAC","AAT"}),
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Aspartic_acid("Aspartic acid","Asp","D",new String[]{"GAT","GAC"}),
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Cysteine("Cysteine","Cys","C",new String[]{"TGC","TGC"}),
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Glutamic_acid("Glutamic acid","Glu","E",new String[]{"GAA","GAG"}),
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Glutamine("Glutamine","Gln","Q",new String[]{"CAA","CAG"}),
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Glycine("Glycine","Gly","G",new String[]{"GGA","GGC","GGG","GGT"}),
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Histidine("Histidine","His","H",new String[]{"CAC","CAT"}),
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Isoleucine("Isoleucine","Ile","I",new String[]{"ATA","ATC","ATT"}),
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Leucine("Leucine","Leu","L",new String[]{"CTA","CTC","CTG","CTT","TTA","TTG"}),
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Lysine("Lysine","Lys","K", new String[]{"AAA","AAG"}),
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Methionine("Methionine","Met","M",new String[]{"ATG"}),
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Phenylalanine("Phenylalanine","Phe","F",new String[]{"TTC","TTT"}),
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Proline("Proline","Pro","P",new String[]{"CCA","CCC","CCG","CCT"}),
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Serine("Serine","Ser","S",new String[]{"AGC","AGT","TCA","TCC","TCG","TCT"}),
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Stop_codon("Stop codon","Stop","*",new String[]{"TAA","TAG","TGA"}),
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Threonine("Threonine","Thr","T",new String[]{"ACA","ACC","ACG","ACT"}),
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Tryptophan("Tryptophan","Trp","W",new String[]{"TGG"}),
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Tyrosine("Tyrosine","Tyr","Y",new String[]{"TAC","TAT"}),
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Valine("Valine","Val","V",new String[]{"GTA","GTC","GTG","GTT"});
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String[] codons;
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String fullName;
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String code;
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String letter;
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AminoAcid(String name, String shortName, String abbrev, String[] myCodons) {
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codons = myCodons;
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fullName = name;
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code = shortName;
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letter = abbrev;
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}
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public String getName() {
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return fullName;
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}
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public String getLetter() {
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return letter;
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}
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public String getCode() {
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return code;
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}
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public boolean isStop() {
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return this == Stop_codon;
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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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}
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package org.broadinstitute.sting.utils.analysis;
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import java.util.HashMap;
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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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public class AminoAcidTable {
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public HashMap<String,AminoAcid> tableByCodon = new HashMap<String,AminoAcid>(21);
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public HashMap<String,AminoAcid> tableByCode = new HashMap<String,AminoAcid>(21);
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public AminoAcidTable() {
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for ( AminoAcid acid : AminoAcid.values() ) {
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tableByCode.put(acid.getCode(),acid);
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for ( String codon : acid.codons ) {
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tableByCodon.put(codon,acid);
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}
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}
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}
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// todo -- these functions are for the genomic annotator and are named too generally -- they are
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// todo -- actually accessors by codon; thus should be more specific.
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public AminoAcid getEukaryoticAA(String codon) {
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return tableByCodon.get(codon.toUpperCase());
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}
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public AminoAcid getMitochondrialAA(String codon, boolean isFirst) {
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String upperCodon = codon.toUpperCase();
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if ( isFirst && upperCodon.equals("ATT") || upperCodon.equals("ATA") ) {
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return AminoAcid.Methionine;
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} else if ( upperCodon.equals("AGA") || upperCodon.equals("AGG") ) {
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return AminoAcid.Stop_codon;
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} else if ( upperCodon.equals("TGA") ) {
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return AminoAcid.Tryptophan;
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} else {
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return tableByCodon.get(upperCodon);
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}
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}
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public AminoAcid getAminoAcidByCode(String code) {
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return tableByCode.get(code);
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}
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}
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@ -0,0 +1,52 @@
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package org.broadinstitute.sting.utils.analysis;
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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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public class AminoAcidUtils {
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public static String[] getAminoAcidNames() {
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String[] names = new String[AminoAcid.values().length];
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for ( AminoAcid acid : AminoAcid.values() ) {
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names[acid.ordinal()] = acid.getName();
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}
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return names;
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}
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public static String[] getAminoAcidCodes() {
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String[] codes = new String[AminoAcid.values().length];
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for ( AminoAcid acid : AminoAcid.values() ) {
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codes[acid.ordinal()] = acid.getCode();
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}
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return codes;
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}
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}
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Reference in New Issue