First pass at a sequenom ROD. Nothing uses it; currently undergoing testing.
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2629 348d0f76-0448-11de-a6fe-93d51630548a
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chartl
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package org.broadinstitute.sting.gatk.refdata;
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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.StingException;
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import java.io.*;
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import java.util.*;
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/**
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* Created by IntelliJ IDEA.
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* User: chartl
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* Date: Jan 19, 2010
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* Time: 10:24:18 AM
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* To change this template use File | Settings | File Templates.
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*/
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public class SequenomRodWithGenomeLoc extends BasicReferenceOrderedDatum implements ReferenceOrderedDatum {
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private final String[] SEQUENOM_HEADER_FIELDS = { "#Family ID", "Individual ID", "Paternal ID", "Maternal ID", "Sex", "Phenotype" } ;
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private ArrayList<SequenomVariantInfo> variants;
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private SequenomVariantInfo currentVariant;
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private ListIterator<SequenomVariantInfo> variantIterator;
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private HashSet headerEntries;
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// // // CONSTRUCTOR // // //
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public SequenomRodWithGenomeLoc(String name) {
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super(name);
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}
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@Override
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public Object initialize(final File seqFile) throws FileNotFoundException {
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if ( ! seqFile.exists() ) {
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throw new FileNotFoundException("File "+seqFile.getAbsolutePath()+" does not exist.");
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}
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headerEntries = new HashSet<String>(Arrays.asList(SEQUENOM_HEADER_FIELDS));
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variants = parseSequenomFile(seqFile);
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if ( variants != null ) {
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variantIterator = variants.listIterator();
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currentVariant = variantIterator.next();
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}
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assertNotNull();
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return null;
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}
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private void assertNotNull() {
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if ( currentVariant == null ) {
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throw new UnsupportedOperationException ( "Current sequenom variant information was set to null" );
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}
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}
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@Override
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public boolean parseLine(Object obj, String[] args) {
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if ( variantIterator.hasNext() ) {
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currentVariant = variantIterator.next();
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return true;
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} else {
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return false;
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}
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}
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@Override
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public GenomeLoc getLocation() {
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return currentVariant.getLocation();
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}
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@Override
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public String toString() {
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return currentVariant == null ? "" : currentVariant.toString();
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}
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public String getVariantName() {
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return currentVariant.getName();
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}
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public ArrayList<String> getVariantSampleNames() {
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return currentVariant.getSampleNames();
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}
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public ArrayList<Genotype> getGenotypes() {
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return currentVariant.getGenotypes();
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}
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private ArrayList<SequenomVariantInfo> parseSequenomFile(File file) {
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try {
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BufferedReader reader = new BufferedReader( new FileReader ( file ) );
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String header = reader.readLine();
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ArrayList<SequenomVariantInfo> seqVars = instantiateVariantListFromHeader(header);
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ArrayList<Integer> snpOffsets = getSNPOffsetsFromHeader(header);
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String line = null;
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do {
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line = reader.readLine();
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incorporateInfo(seqVars,snpOffsets,line);
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} while ( line != null );
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java.util.Collections.sort(seqVars); // because the comparable uses the GenomeLoc comparable; these
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// are sorted in standard reference order
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return seqVars;
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} catch ( FileNotFoundException e ) {
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throw new StingException("File "+file.getAbsolutePath()+" could not be found. This was checked earlier. Should never happen.",e);
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} catch ( IOException e ) {
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throw new StingException("Error reading file "+file.getAbsolutePath()+".",e);
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}
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}
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private void incorporateInfo(List<SequenomVariantInfo> vars, List<Integer> offsets, String seqLine) {
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String[] genotypes = seqLine.split("\t");
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String individualName = genotypes[1];
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int snpNumber = 0;
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for ( int i : offsets ) {
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vars.get(snpNumber).addGenotypeEntry(genotypes[i], individualName);
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snpNumber++;
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}
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}
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private ArrayList<SequenomVariantInfo> instantiateVariantListFromHeader(String header) {
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ArrayList<SequenomVariantInfo> seqVars = new ArrayList<SequenomVariantInfo>();
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String[] headerFields = header.split("\t");
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for ( String field : headerFields ) {
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if ( ! headerEntries.contains(field) ) {
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// not a standard header, so a variant
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seqVars.add(new SequenomVariantInfo(field));
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}
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}
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return seqVars;
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}
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private ArrayList<Integer> getSNPOffsetsFromHeader(String header) {
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ArrayList<Integer> offsets = new ArrayList<Integer>();
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String[] headerFields = header.split("\t");
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int offset = 0;
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for ( String field : headerFields ) {
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if ( ! headerEntries.contains(field) ) {
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offsets.add(offset);
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}
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offset++;
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}
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return offsets;
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}
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}
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class SequenomVariantInfo implements Comparable {
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private String variantName;
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private GenomeLoc loc;
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private ArrayList<Genotype> genotypes;
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private ArrayList<String> sampleNames;
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public GenomeLoc getLocation() {
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return loc;
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}
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public String getName() {
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return variantName;
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}
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public ArrayList<String> getSampleNames() {
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return sampleNames;
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}
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public ArrayList<Genotype> getGenotypes() {
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return genotypes;
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}
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// CONSTRUCTOR
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public SequenomVariantInfo(String variantName) {
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this.variantName = variantName;
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this.parseNameToLoc();
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}
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private void parseNameToLoc() {
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String chrom = this.variantName.split("_c")[1].split("_")[0];
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String pos = this.variantName.split("_p")[1].split("_")[0];
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this.loc = GenomeLocParser.parseGenomeLoc(chrom+":"+pos);
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}
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public void addGenotypeEntry(String genotypeString, String sampleName) {
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String[] alleleStrs = genotypeString.split(" ");
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ArrayList<Allele> alleles = new ArrayList<Allele>(2); // most, if not all, will be bi-allelic
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for ( String alStr : alleleStrs ) {
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Allele.AlleleType type = alStr.indexOf("-") > -1 ? Allele.AlleleType.DELETION : alStr.length() > 1 ? Allele.AlleleType.INSERTION : Allele.AlleleType.SNP;
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alleles.add(new Allele(type,alStr));
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}
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this.genotypes.add( new Genotype(alleles, sampleName, 20.0));
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this.sampleNames.add(sampleName);
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}
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public int compareTo(Object obj) {
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if ( ! ( obj instanceof SequenomVariantInfo ) ) {
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return 1;
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}
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return loc.compareTo(((SequenomVariantInfo) obj).getLocation());
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}
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}
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