Added support for MAF features. So far works for MAF Lite only, annotated MAF is NOT TESTED yet AT ALL.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@5105 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache
parent
91e4bb0285
commit
f036a178f1
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@ -11,6 +11,7 @@ import org.broad.tribble.vcf.*;
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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.utils.helpers.DbSNPHelper;
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import org.broadinstitute.sting.playground.gatk.features.maf.MafFeature;
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import java.util.*;
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@ -42,6 +43,7 @@ public class VariantContextAdaptors {
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adaptors.put(HapMapFeature.class, new HapMapAdaptor());
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adaptors.put(GeliTextFeature.class, new GeliTextAdaptor());
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adaptors.put(VariantContext.class, new VariantContextAdaptor());
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adaptors.put(MafFeature.class, new MafAdaptor());
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}
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public static boolean canBeConvertedToVariantContext(Object variantContainingObject) {
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@ -279,4 +281,83 @@ public class VariantContextAdaptors {
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return vc;
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}
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}
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private static class MafAdaptor extends VCAdaptor {
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/**
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* convert to a Variant Context, given:
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* @param name the name of the ROD
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* @param input the Rod object, in this case a MafFeature
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* @return a VariantContext object
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*/
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// VariantContext convert(String name, Object input) {
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// return convert(name, input, null);
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// }
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/**
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* convert to a Variant Context, given:
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* @param name the name of the ROD
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* @param input the Rod object, in this case a MafFeature
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* @param ref the reference context
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* @return a VariantContext object
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*/
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VariantContext convert(String name, Object input, ReferenceContext ref) {
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if ( ref == null )
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throw new UnsupportedOperationException("Conversion from MAF to VariantContext requires a reference context, null received");
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MafFeature maf = (MafFeature)input;
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if ( ! Allele.acceptableAlleleBases(maf.getRefBases(),true) )
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return null;
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List<Allele> alleles = new ArrayList<Allele>();
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Allele refAllele = Allele.create(maf.getRefBases(), true);
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// add the reference allele:
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alleles.add(refAllele);
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// add all of the alt alleles
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for ( String alt : maf.getAllNonRefAlleleList() ) {
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if ( ! Allele.acceptableAlleleBases(alt,false) ) {
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//System.out.printf("Excluding dbsnp record %s%n", dbsnp);
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return null;
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}
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alleles.add(Allele.create(alt, false));
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}
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// make a mapping from sample to genotype
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String normalSample = maf.getNormalSampleId();
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String tumorSample = maf.getTumorSampleId();
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// String[] genotypeStrings = hapmap.getGenotypes();
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Map<String, Genotype> genotypes = new HashMap<String, Genotype>(2);
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addGenotype(genotypes, normalSample, maf.getObservedNormalAlleleList(),maf.getRefBases());
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addGenotype(genotypes,tumorSample,maf.getObservedTumorAlleleList(),maf.getRefBases());
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HashMap<String, Object> attrs = new HashMap<String, Object>(1);
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// attrs.put(VariantContext.ID_KEY, hapmap.getName());
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int end = maf.getEnd();
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VariantContext vc = new VariantContext(name, maf.getChr(), maf.getStart(), end, alleles,
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genotypes, VariantContext.NO_NEG_LOG_10PERROR, null, attrs);
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return vc;
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}
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private void addGenotype(Map<String,Genotype> dest, String sampleId, List<String> alleles, String refAllele) {
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List<Allele> myAlleles = new ArrayList<Allele>(2);
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boolean success = true;
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for ( String a : alleles ) {
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if ( a.isEmpty() || a.contains("N") || a.contains(".")) return; // bad allele found
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myAlleles.add(Allele.create(a,refAllele.equals(a)));
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}
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dest.put(sampleId, new Genotype(sampleId,myAlleles));
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}
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}
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}
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@ -0,0 +1,300 @@
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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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package org.broadinstitute.sting.playground.gatk.features.maf;
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import org.broad.tribble.FeatureCodec;
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import org.broad.tribble.Feature;
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import org.broad.tribble.readers.LineReader;
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import org.apache.log4j.Logger;
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import org.broadinstitute.sting.utils.exceptions.UserException;
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import java.io.IOException;
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import java.util.Map;
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import java.util.HashMap;
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/**
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* Created by IntelliJ IDEA.
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* User: asivache
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* Date: Jan 24, 2011
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* Time: 12:04:10 PM
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* To change this template use File | Settings | File Templates.
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*/
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public class MafCodec implements FeatureCodec {
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private final static Logger log = Logger.getLogger(MafCodec.class);
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private int expectedTokenCount = -1;
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private int BUILD_COL;
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private int CHR_COL;
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private int START_COL;
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private int END_COL;
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private int REF_ALLELE_COL;
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private int TUMOR_ALLELE1_COL;
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private int TUMOR_ALLELE2_COL;
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private int TUMOR_SAMPLE_COL;
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private int NORMAL_SAMPLE_COL;
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// optional fields (absent from maf lite):
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private int VARTYPE_COL = -1;
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private int STRAND_COL = -1;
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private static String BUILD_COLNAME="NCBI_Build";
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private static String CHR_COLNAME="Chromosome";
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private static String START_COLNAME="Start_position";
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private static String END_COLNAME="End_position";
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private static String REF_ALLELE_COLNAME="Reference_Allele";
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private static String TUMOR_ALLELE1_COLNAME="Tumor_Seq_Allele1";
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private static String TUMOR_ALLELE2_COLNAME="Tumor_Seq_Allele2";
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private static String TUMOR_SAMPLE_COLNAME="Tumor_Sample_Barcode";
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private static String NORMAL_SAMPLE_COLNAME="Matched_Norm_Sample_Barcode";
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// optional fields (absent from maf lite):
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private static String VARTYPE_COLNAME="Variant_Type";
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private static String STRAND_COLNAME="Strand";
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public enum MAF_TYPE {
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UNKNOWN,LITE, ANNOTATED
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}
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private static String INS ="INS";
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private static String DEL ="DEL";
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private static String SNP ="SNP";
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private static String MNP ="MNP";
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private MAF_TYPE mafType=MAF_TYPE.UNKNOWN;
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/**
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* Decode a line to obtain just its FeatureLoc for indexing -- contig, start, and stop.
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*
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* @param line the input line to decode
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* @return Return the FeatureLoc encoded by the line, or null if the line does not represent a feature (e.g. is
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* a comment)
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*/
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public Feature decodeLoc(String line) {
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return decode(line);
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}
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public Feature decode(String line) {
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// ignore commented-out lines
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if (line.startsWith("#")) return null;
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// split the line
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String[] tokens = line.split("\\t");
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if ( expectedTokenCount == -1 ) { // do this only when we receive the first line and do not know the number of columns yet
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// we have not seen a single line yet, let's initialize the number of fields from the first line:
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expectedTokenCount = tokens.length;
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if ( expectedTokenCount == 9 ) {
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mafType = MAF_TYPE.LITE;
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log.info("MAF file appears to be MAF Lite");
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} else {
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if ( expectedTokenCount == 63 ) {
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mafType = MAF_TYPE.ANNOTATED;
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log.info("MAF file appears to be MAF-Annotated");
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} else {
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log.info("MAF file has "+expectedTokenCount +" columns, unknown file type");
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}
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}
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if ( line.contains("Chromosome") && line.contains("Start") && line.contains("Build")) {
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// a naive way to detect the line with column names
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setColumnsFromHeader(tokens);
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log.info("MAF file contains header, all required columns found!");
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return null;
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} else {
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switch( mafType ) {
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case UNKNOWN: throw new UserException.MalformedFile("Can not guess type of the MAF file from number of columns and there is no header");
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case LITE: setMafLiteCols(); break;
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case ANNOTATED: setMafAnnotatedCols(); break;
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}
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log.info("MAF file has no header; assuming standard column order for the MAF type "+mafType);
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}
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}
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if (tokens.length != expectedTokenCount) {
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log.error("MAF line contains wrong number of columns");
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return null;
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}
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// create a new feature from the line:
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int start = Integer.valueOf(tokens[START_COL]);
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int stop = Integer.valueOf(tokens[END_COL]);
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String eventType="UNKNOWN";
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String ref = tokens[REF_ALLELE_COL];
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String alt1 = tokens[TUMOR_ALLELE1_COL];
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String alt2 = tokens[TUMOR_ALLELE2_COL];
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if ( ref.equals("-") ) {
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// insertion
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eventType = INS;
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stop-- ; // maf lists stop as first base after insertion, convert internally to vcf style
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// perform some format validation:
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if ( alt1.equals("-") && alt2.equals("-") )
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throw new UserException.MalformedFile("Inconsistency in MAF: both alt alleles reported as ref ('-') for an insertion");
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if ( ! alt1.equals("-") && ! alt2.equals("-") && ! alt1.equals(alt2) )
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throw new UserException.MalformedFile("Inconsistency in MAF: two different (non-ref) alt alleles reported for an insertion");
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if ( stop != start )
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throw new UserException.MalformedFile("Inconsistency in MAF: end position for an insertion is not start+1");
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} else {
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if ( alt1.equals("-") || alt2.equals("-") ) {
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// deletion
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eventType = DEL;
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start--; // maf lists start as the first deleted base; convert internally to vcf style
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// perform some format validation:
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if ( ! alt1.equals("-") && ! alt1.equals(ref) )
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throw new UserException.MalformedFile("Inconsistency in MAF: non-deleted alt allele is not ref for a deletion");
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if ( ! alt2.equals("-") && ! alt2.equals(ref) )
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throw new UserException.MalformedFile("Inconsistency in MAF: non-deleted alt allele is not ref for a deletion");
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if ( (stop - start) != ref.length() )
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throw new UserException.MalformedFile("Inconsistency in MAF: deletion length is not end-start+1");
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} else {
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// no '-' alleles --> it's a snp/mnp
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if ( ref.length() == 1 ) {
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// it's a snp
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eventType = SNP;
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if ( stop != start )
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throw new UserException.MalformedFile("Inconsistency in MAF: start/end positions not equal for a SNP");
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} else {
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// it's an mnp
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eventType = MNP;
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if ( (stop - start + 1) != ref.length() )
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throw new UserException.MalformedFile("Inconsistency in MAF: MNP length is not end-start+1");
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}
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if ( alt1.length() != ref.length() || alt2.length() != ref.length() )
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throw new UserException.MalformedFile("Inconsistency in MAF: lengths of ref and alt alleles for a SNP/MNP differ");
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if ( ! alt1.equals(ref) && ! alt2.equals(ref) && ! alt1.equals(alt2) )
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throw new UserException.MalformedFile("Inconsistency in MAF: two different non-ref alt alleles reported for a SNP/MNP");
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}
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}
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// if we got vartype column, make sure it makes sense:
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if ( VARTYPE_COL != -1 && ! tokens[VARTYPE_COL].equals(eventType) )
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throw new UserException.MalformedFile("Inconsistency in MAF: variant looks like a "+eventType +" but annotated as "+
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tokens[VARTYPE_COL]);
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MafFeature feature = new MafFeature(tokens[CHR_COL],start,stop);
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feature.setVariantType(eventType);
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feature.setRefAllele(ref);
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feature.setObservedTumor(alt1,alt2);
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feature.setTumorSample(tokens[TUMOR_SAMPLE_COL]);
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feature.setNormalSample(tokens[NORMAL_SAMPLE_COL]);
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return feature;
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}
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public Class getFeatureType() {
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return MafFeature.class;
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}
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/** Read and return the header, or null if there is no header.
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*
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* @return header object
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*/
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public Object readHeader(LineReader reader) {
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return null;
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}
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/** Set expected column indices for MafLite
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*
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*/
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private void setMafLiteCols() {
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BUILD_COL = 0;
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CHR_COL = 1;
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START_COL = 2;
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END_COL = 3;
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REF_ALLELE_COL = 4;
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TUMOR_ALLELE1_COL = 5;
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TUMOR_ALLELE2_COL = 6;
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TUMOR_SAMPLE_COL = 7;
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NORMAL_SAMPLE_COL = 8;
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}
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private void setMafAnnotatedCols() {
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BUILD_COL = 3;
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CHR_COL = 4;
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START_COL = 5;
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END_COL = 6;
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REF_ALLELE_COL = 10;
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TUMOR_ALLELE1_COL = 11;
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TUMOR_ALLELE2_COL = 12;
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TUMOR_SAMPLE_COL = 15;
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NORMAL_SAMPLE_COL = 16;
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VARTYPE_COL = 9;
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STRAND_COL = 7;
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}
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private void setColumnsFromHeader(String[] tokens) {
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Map<String,Integer> colNames = new HashMap<String,Integer>();
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for ( int i = 0 ; i < tokens.length ; i++ ) colNames.put(tokens[i],i);
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if ( colNames.containsKey(BUILD_COLNAME) ) BUILD_COL = colNames.get(BUILD_COLNAME);
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else throw new UserException.MalformedFile("Maf file does not have "+BUILD_COLNAME+" column");
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if ( colNames.containsKey(CHR_COLNAME) ) CHR_COL = colNames.get(CHR_COLNAME);
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else throw new UserException.MalformedFile("Maf file does not have "+CHR_COLNAME+" column");
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if ( colNames.containsKey(START_COLNAME) ) START_COL = colNames.get(START_COLNAME);
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else throw new UserException.MalformedFile("Maf file does not have "+START_COLNAME+" column");
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if ( colNames.containsKey(END_COLNAME) ) END_COL = colNames.get(END_COLNAME);
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else throw new UserException.MalformedFile("Maf file does not have "+END_COLNAME+" column");
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if ( colNames.containsKey(REF_ALLELE_COLNAME) ) REF_ALLELE_COL = colNames.get(REF_ALLELE_COLNAME);
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else throw new UserException.MalformedFile("Maf file does not have "+REF_ALLELE_COLNAME+" column");
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if ( colNames.containsKey(TUMOR_ALLELE1_COLNAME) ) TUMOR_ALLELE1_COL = colNames.get(TUMOR_ALLELE1_COLNAME);
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else throw new UserException.MalformedFile("Maf file does not have "+TUMOR_ALLELE1_COLNAME+" column");
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if ( colNames.containsKey(TUMOR_ALLELE2_COLNAME) ) TUMOR_ALLELE2_COL = colNames.get(TUMOR_ALLELE2_COLNAME);
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else throw new UserException.MalformedFile("Maf file does not have "+TUMOR_ALLELE2_COLNAME+" column");
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if ( colNames.containsKey(TUMOR_SAMPLE_COLNAME) ) TUMOR_SAMPLE_COL = colNames.get(TUMOR_SAMPLE_COLNAME);
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else throw new UserException.MalformedFile("Maf file does not have "+TUMOR_SAMPLE_COLNAME+" column");
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if ( colNames.containsKey(NORMAL_SAMPLE_COLNAME) ) NORMAL_SAMPLE_COL = colNames.get(NORMAL_SAMPLE_COLNAME);
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else throw new UserException.MalformedFile("Maf file does not have "+NORMAL_SAMPLE_COLNAME+" column");
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// we do not require variant type column but we use it if it's present (for validation):
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if ( colNames.containsKey(VARTYPE_COLNAME) ) VARTYPE_COL = colNames.get(VARTYPE_COLNAME);
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// we do not require strand column but we use it if it's present (for validation):
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if ( colNames.containsKey(STRAND_COLNAME) ) STRAND_COL = colNames.get(STRAND_COLNAME);
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}
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}
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@ -0,0 +1,206 @@
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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
|
||||
* obtaining a copy of this software and associated documentation
|
||||
* files (the "Software"), to deal in the Software without
|
||||
* restriction, including without limitation the rights to use,
|
||||
* copy, modify, merge, publish, distribute, sublicense, and/or sell
|
||||
* copies of the Software, and to permit persons to whom the
|
||||
* Software is furnished to do so, subject to the following
|
||||
* conditions:
|
||||
*
|
||||
* The above copyright notice and this permission notice shall be
|
||||
* included in all copies or substantial portions of the Software.
|
||||
*
|
||||
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND,
|
||||
* EXPRESS OR IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES
|
||||
* OF MERCHANTABILITY, FITNESS FOR A PARTICULAR PURPOSE AND
|
||||
* NONINFRINGEMENT. IN NO EVENT SHALL THE AUTHORS OR COPYRIGHT
|
||||
* HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER LIABILITY,
|
||||
* WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING
|
||||
* FROM, OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR
|
||||
* OTHER DEALINGS IN THE SOFTWARE.
|
||||
*/
|
||||
|
||||
package org.broadinstitute.sting.playground.gatk.features.maf;
|
||||
|
||||
import org.broad.tribble.Feature;
|
||||
import org.broadinstitute.sting.utils.exceptions.StingException;
|
||||
|
||||
import java.util.*;
|
||||
|
||||
/**
|
||||
* Created by IntelliJ IDEA.
|
||||
* User: asivache
|
||||
* Date: Jan 24, 2011
|
||||
* Time: 12:01:12 PM
|
||||
* To change this template use File | Settings | File Templates.
|
||||
*/
|
||||
public class MafFeature implements Feature {
|
||||
private String contig; // our contig location
|
||||
private int start; // our starting location, zero based
|
||||
private int stop; // our stopping location
|
||||
|
||||
private String refAllele = "."; // the reference allele
|
||||
private String[] observedTumAlleles = null; // The sequences of the observed alleles in tumor
|
||||
private String[] observedNormAlleles = null; // The sequences of the observed alleles in normal
|
||||
private String tumorSampleId = null;
|
||||
private String normalSampleId = null;
|
||||
|
||||
public enum Type {
|
||||
UNKNOWN,SNP,MNP,INS,DEL
|
||||
};
|
||||
|
||||
private Type type = Type.UNKNOWN;
|
||||
|
||||
/**
|
||||
* create the dbSNP feature, given the following information:
|
||||
*
|
||||
* @param contig the contig rsID
|
||||
* @param start the start position, one based
|
||||
* @param stop the stop position, one based
|
||||
*/
|
||||
MafFeature(String contig,
|
||||
int start,
|
||||
int stop) {
|
||||
this.contig = contig;
|
||||
this.start = start;
|
||||
this.stop = stop;
|
||||
}
|
||||
|
||||
public void setVariantType(String t) {
|
||||
type=Type.valueOf(t);
|
||||
}
|
||||
|
||||
public void setObservedTumor(String[] obs) {
|
||||
observedTumAlleles = obs;
|
||||
}
|
||||
|
||||
public void setObservedTumor(String allele1, String allele2) {
|
||||
observedTumAlleles = new String[2];
|
||||
observedTumAlleles[0] = allele1;
|
||||
observedTumAlleles[1] = allele2;
|
||||
}
|
||||
|
||||
public void setRefAllele(String ref) {
|
||||
this.refAllele = ref;
|
||||
}
|
||||
|
||||
public void setTumorSample(String sampleId) {
|
||||
this.tumorSampleId = sampleId;
|
||||
}
|
||||
|
||||
public void setNormalSample(String sampleId) {
|
||||
this.normalSampleId = sampleId;
|
||||
}
|
||||
|
||||
public String getRefBases() {
|
||||
return refAllele;
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns list of alleles (represented as strings) observed in Tumor. Returned alleles
|
||||
* could be redundant (e.g. if we have homozygous non-ref at ploidy 2+).
|
||||
* @return
|
||||
*/
|
||||
public List<String> getObservedTumorAlleleList() {
|
||||
return Arrays.asList(observedTumAlleles);
|
||||
}
|
||||
|
||||
/**
|
||||
* Returns list of alleles (represented as strings) observed in Tumor. Returned alleles
|
||||
* could be redundant (e.g. if we have homozygous non-ref at ploidy 2+).
|
||||
* @return
|
||||
*/
|
||||
public List<String> getObservedNormalAlleleList() {
|
||||
if ( observedNormAlleles == null ) {
|
||||
// if we got no ref allele observations recorded in the maf, we assume its ref/ref (somatic event)
|
||||
List<String> l = new ArrayList<String>(2);
|
||||
l.add(refAllele);
|
||||
l.add(refAllele);
|
||||
return l;
|
||||
}
|
||||
else return Arrays.asList(observedTumAlleles);
|
||||
}
|
||||
|
||||
/** Returns a (non-redundant) list of all distinct alleles
|
||||
* observed at the site, plus a reference allele (whether it
|
||||
* was actually observed or not). The reference allele is always returned as first
|
||||
* element of the list.
|
||||
* @return
|
||||
*/
|
||||
public List<String> getAllAlleleList() {
|
||||
List<String> l = new ArrayList<String>();
|
||||
l.add(refAllele);
|
||||
for ( String a : observedTumAlleles ) {
|
||||
if ( l.contains(a) ) continue;
|
||||
l.add(a);
|
||||
}
|
||||
if ( observedNormAlleles != null ) {
|
||||
for ( String a : observedNormAlleles ) {
|
||||
if ( l.contains(a) ) continue; // already have this allele
|
||||
l.add(a);
|
||||
}
|
||||
}
|
||||
return l;
|
||||
}
|
||||
|
||||
/** Returns a (non-redundant) list of all distinct non-reference alleles
|
||||
* observed at the site
|
||||
* @return
|
||||
*/
|
||||
public List<String> getAllNonRefAlleleList() {
|
||||
List<String> l = new ArrayList<String>();
|
||||
for ( String a : observedTumAlleles ) {
|
||||
if ( l.contains(a) ) continue; // already have this allele
|
||||
if ( a.equals(refAllele)) continue; // allele is ref, we do not need it
|
||||
l.add(a);
|
||||
}
|
||||
if ( observedNormAlleles != null ) {
|
||||
for ( String a : observedNormAlleles ) {
|
||||
if ( l.contains(a) ) continue; // already have this allele
|
||||
if ( a.equals(refAllele)) continue; // allele is ref, we do not need it
|
||||
l.add(a);
|
||||
}
|
||||
}
|
||||
return l;
|
||||
}
|
||||
|
||||
public String getTumorSampleId() { return tumorSampleId; }
|
||||
public String getNormalSampleId() { return normalSampleId; }
|
||||
|
||||
public boolean isRefAllele(String a) { return refAllele.equals(a); }
|
||||
|
||||
public Type getType() { return type; }
|
||||
|
||||
public int lengthOnRef() {
|
||||
switch ( type ) {
|
||||
case SNP:
|
||||
case MNP:
|
||||
case DEL:
|
||||
return refAllele.length();
|
||||
case INS:
|
||||
return 0;
|
||||
default:
|
||||
throw new StingException("Unrecognized event type in Maf record: "+type);
|
||||
}
|
||||
}
|
||||
|
||||
/*
|
||||
* the required getting and setter methods
|
||||
*/
|
||||
|
||||
public String getChr() {
|
||||
return contig;
|
||||
}
|
||||
|
||||
public int getStart() {
|
||||
return start;
|
||||
}
|
||||
|
||||
public int getEnd() {
|
||||
return stop;
|
||||
}
|
||||
|
||||
}
|
||||
Loading…
Reference in New Issue