Simple walker to look at SNPs near indels. Didn't need to make this a walker and commit it, but used it as an opportunity to play with GIT in unstable.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@6049 348d0f76-0448-11de-a6fe-93d51630548a
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/*
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* Copyright (c) 2010.
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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
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* THE USE OR OTHER DEALINGS IN THE SOFTWARE.
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*/
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package org.broadinstitute.sting.oneoffprojects.walkers;
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import org.broad.tribble.util.variantcontext.VariantContext;
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import org.broad.tribble.vcf.VCFHeader;
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import org.broad.tribble.vcf.VCFHeaderLine;
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import org.broad.tribble.vcf.VCFWriter;
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import org.broadinstitute.sting.commandline.Output;
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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.iterators.DownsampleIterator;
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import org.broadinstitute.sting.gatk.refdata.RefMetaDataTracker;
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import org.broadinstitute.sting.gatk.walkers.Reference;
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import org.broadinstitute.sting.gatk.walkers.Requires;
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import org.broadinstitute.sting.gatk.walkers.RodWalker;
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import org.broadinstitute.sting.gatk.walkers.Window;
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import org.broadinstitute.sting.utils.BaseUtils;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.GenomeLocParser;
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import org.broadinstitute.sting.utils.vcf.VCFUtils;
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import java.io.PrintStream;
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import java.io.Writer;
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import java.security.PrivilegedActionException;
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import java.util.*;
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/**
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* Assesses distance of SNP calls to nearest indel call in Exomes.
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* Use -B:snps,vcf and -B:indels,vcf
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*/
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public class AssessSnpsNearIndels extends RodWalker<Integer, Integer> {
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private class TiTv {
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int TiCount = 0, TvCount = 0;
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public TiTv() {};
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}
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private static final int Bin0to5 = 0;
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private static final int Bin6to10 = 1;
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private static final int Bin11to15 = 2;
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private static final int Bin16to20 = 3;
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private static final int Bin21to25 = 4;
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private static final int Bin26to30 = 5;
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private static final int BinMoreThan30 = 6;
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private GenomeLoc previousIndel = null;
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private ArrayList<VariantContext> snpQueue = new ArrayList<VariantContext>();
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private TiTv[] counts = new TiTv[7];
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private GenomeLocParser GLparser = null;
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@Output(doc="File to which results should be written",required=true)
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protected PrintStream out = null;
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public void initialize() {
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GLparser = getToolkit().getGenomeLocParser();
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for (int i = 0; i < 7; i++)
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counts[i] = new TiTv();
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}
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public Integer map(RefMetaDataTracker tracker, ReferenceContext ref, AlignmentContext context) {
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if ( tracker == null ) // RodWalkers can make funky map calls
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return 0;
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VariantContext snp = tracker.getVariantContext(ref, "snps", null, ref.getLocus(), true);
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VariantContext indel = tracker.getVariantContext(ref, "indels", null, ref.getLocus(), true);
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// first add the snp if available
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if ( snp != null && !snp.isFiltered() ) {
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// flush the queue on a new contig
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if ( !snpQueue.isEmpty() && !snpQueue.get(0).getChr().equals(snp.getChr()) ) {
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for ( VariantContext vc : snpQueue )
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calculateDistance(vc, previousIndel, null);
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snpQueue.clear();
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}
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snpQueue.add(snp);
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}
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// then look for the indel
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if ( indel != null && !indel.isFiltered() ) {
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GenomeLoc loc = GLparser.createGenomeLoc(indel.getChr(), indel.getStart(), indel.getEnd());
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boolean sameContig = !snpQueue.isEmpty() && snpQueue.get(0).getChr().equals(indel.getChr());
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// flush the queue
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for ( VariantContext vc : snpQueue )
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calculateDistance(vc, previousIndel, sameContig ? loc : null);
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snpQueue.clear();
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previousIndel = loc;
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}
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return 1;
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}
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private void calculateDistance(VariantContext snp, GenomeLoc previousIndel, GenomeLoc nextIndel) {
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GenomeLoc loc = GLparser.createGenomeLoc(snp.getChr(), snp.getStart(), snp.getEnd());
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int previousDistance = -1, nextDistance = -1;
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if ( previousIndel != null ) {
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// watch out for spanning deletions
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if ( previousIndel.getStop() > snp.getStart() )
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previousDistance = 0;
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else
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previousDistance = snp.getStart() - previousIndel.getStop();
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}
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if ( nextIndel != null )
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nextDistance = nextIndel.getStart() - loc.getStart();
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if ( previousDistance == -1 && nextDistance == -1 )
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return;
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int distance = -1;
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if ( previousDistance == -1 )
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distance = nextDistance;
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else if ( nextDistance == -1 )
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distance = previousDistance;
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else
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distance = Math.min(previousDistance, nextDistance);
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TiTv obj;
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if ( distance < 0 )
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throw new IllegalStateException("Found a negative distance at " + loc);
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else if ( distance < 6 )
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obj = counts[Bin0to5];
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else if ( distance < 11 )
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obj = counts[Bin6to10];
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else if ( distance < 16 )
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obj = counts[Bin11to15];
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else if ( distance < 21 )
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obj = counts[Bin16to20];
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else if ( distance < 26 )
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obj = counts[Bin21to25];
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else if ( distance < 31 )
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obj = counts[Bin26to30];
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else
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obj = counts[BinMoreThan30];
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if ( BaseUtils.isTransition(snp.getReference().getBases()[0], snp.getAlternateAllele(0).getBases()[0]) )
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obj.TiCount++;
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else
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obj.TvCount++;
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}
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public Integer reduceInit() {
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return 0;
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}
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public Integer reduce(Integer counter, Integer sum) {
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return counter + sum;
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}
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public void onTraversalDone(Integer sum) {
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// flush the queue
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for ( VariantContext vc : snpQueue )
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calculateDistance(vc, previousIndel, null);
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out.println("Bin\tnumTi\tnumTv\tTi/Tv");
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printLine(counts[Bin0to5], "0to5");
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printLine(counts[Bin6to10], "6to10");
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printLine(counts[Bin11to15], "11to15");
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printLine(counts[Bin16to20], "16to20");
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printLine(counts[Bin21to25], "21to25");
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printLine(counts[Bin26to30], "26to30");
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printLine(counts[BinMoreThan30], ">30");
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}
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private void printLine(TiTv obj, String s) {
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out.println(String.format("%s\t%d\t%d\t%.2f", s, obj.TiCount, obj.TvCount, ((double)obj.TiCount/(double)obj.TvCount)));
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}
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}
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