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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 2010-01-19 17:09:36 +00:00
parent 1488578617
commit 53352e1bb4
1 changed files with 208 additions and 0 deletions
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java/src/org/broadinstitute/sting/gatk/refdata/SequenomRodWithGenomeLoc.java 100644
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package org.broadinstitute.sting.gatk.refdata;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.GenomeLocParser;
import org.broadinstitute.sting.utils.StingException;
import java.io.*;
import java.util.*;
/**
* Created by IntelliJ IDEA.
* User: chartl
* Date: Jan 19, 2010
* Time: 10:24:18 AM
* To change this template use File | Settings | File Templates.
*/
public class SequenomRodWithGenomeLoc extends BasicReferenceOrderedDatum implements ReferenceOrderedDatum {
private final String[] SEQUENOM_HEADER_FIELDS = { "#Family ID", "Individual ID", "Paternal ID", "Maternal ID", "Sex", "Phenotype" } ;
private ArrayList<SequenomVariantInfo> variants;
private SequenomVariantInfo currentVariant;
private ListIterator<SequenomVariantInfo> variantIterator;
private HashSet headerEntries;
// // // CONSTRUCTOR // // //
public SequenomRodWithGenomeLoc(String name) {
super(name);
}
@Override
public Object initialize(final File seqFile) throws FileNotFoundException {
if ( ! seqFile.exists() ) {
throw new FileNotFoundException("File "+seqFile.getAbsolutePath()+" does not exist.");
}
headerEntries = new HashSet<String>(Arrays.asList(SEQUENOM_HEADER_FIELDS));
variants = parseSequenomFile(seqFile);
if ( variants != null ) {
variantIterator = variants.listIterator();
currentVariant = variantIterator.next();
}
assertNotNull();
return null;
}
private void assertNotNull() {
if ( currentVariant == null ) {
throw new UnsupportedOperationException ( "Current sequenom variant information was set to null" );
}
}
@Override
public boolean parseLine(Object obj, String[] args) {
if ( variantIterator.hasNext() ) {
currentVariant = variantIterator.next();
return true;
} else {
return false;
}
}
@Override
public GenomeLoc getLocation() {
return currentVariant.getLocation();
}
@Override
public String toString() {
return currentVariant == null ? "" : currentVariant.toString();
}
public String getVariantName() {
return currentVariant.getName();
}
public ArrayList<String> getVariantSampleNames() {
return currentVariant.getSampleNames();
}
public ArrayList<Genotype> getGenotypes() {
return currentVariant.getGenotypes();
}
private ArrayList<SequenomVariantInfo> parseSequenomFile(File file) {
try {
BufferedReader reader = new BufferedReader( new FileReader ( file ) );
String header = reader.readLine();
ArrayList<SequenomVariantInfo> seqVars = instantiateVariantListFromHeader(header);
ArrayList<Integer> snpOffsets = getSNPOffsetsFromHeader(header);
String line = null;
do {
line = reader.readLine();
incorporateInfo(seqVars,snpOffsets,line);
} while ( line != null );
java.util.Collections.sort(seqVars); // because the comparable uses the GenomeLoc comparable; these
// are sorted in standard reference order
return seqVars;
} catch ( FileNotFoundException e ) {
throw new StingException("File "+file.getAbsolutePath()+" could not be found. This was checked earlier. Should never happen.",e);
} catch ( IOException e ) {
throw new StingException("Error reading file "+file.getAbsolutePath()+".",e);
}
}
private void incorporateInfo(List<SequenomVariantInfo> vars, List<Integer> offsets, String seqLine) {
String[] genotypes = seqLine.split("\t");
String individualName = genotypes[1];
int snpNumber = 0;
for ( int i : offsets ) {
vars.get(snpNumber).addGenotypeEntry(genotypes[i], individualName);
snpNumber++;
}
}
private ArrayList<SequenomVariantInfo> instantiateVariantListFromHeader(String header) {
ArrayList<SequenomVariantInfo> seqVars = new ArrayList<SequenomVariantInfo>();
String[] headerFields = header.split("\t");
for ( String field : headerFields ) {
if ( ! headerEntries.contains(field) ) {
// not a standard header, so a variant
seqVars.add(new SequenomVariantInfo(field));
}
}
return seqVars;
}
private ArrayList<Integer> getSNPOffsetsFromHeader(String header) {
ArrayList<Integer> offsets = new ArrayList<Integer>();
String[] headerFields = header.split("\t");
int offset = 0;
for ( String field : headerFields ) {
if ( ! headerEntries.contains(field) ) {
offsets.add(offset);
}
offset++;
}
return offsets;
}
}
class SequenomVariantInfo implements Comparable {
private String variantName;
private GenomeLoc loc;
private ArrayList<Genotype> genotypes;
private ArrayList<String> sampleNames;
public GenomeLoc getLocation() {
return loc;
}
public String getName() {
return variantName;
}
public ArrayList<String> getSampleNames() {
return sampleNames;
}
public ArrayList<Genotype> getGenotypes() {
return genotypes;
}
// CONSTRUCTOR
public SequenomVariantInfo(String variantName) {
this.variantName = variantName;
this.parseNameToLoc();
}
private void parseNameToLoc() {
String chrom = this.variantName.split("_c")[1].split("_")[0];
String pos = this.variantName.split("_p")[1].split("_")[0];
this.loc = GenomeLocParser.parseGenomeLoc(chrom+":"+pos);
}
public void addGenotypeEntry(String genotypeString, String sampleName) {
String[] alleleStrs = genotypeString.split(" ");
ArrayList<Allele> alleles = new ArrayList<Allele>(2); // most, if not all, will be bi-allelic
for ( String alStr : alleleStrs ) {
Allele.AlleleType type = alStr.indexOf("-") > -1 ? Allele.AlleleType.DELETION : alStr.length() > 1 ? Allele.AlleleType.INSERTION : Allele.AlleleType.SNP;
alleles.add(new Allele(type,alStr));
}
this.genotypes.add( new Genotype(alleles, sampleName, 20.0));
this.sampleNames.add(sampleName);
}
public int compareTo(Object obj) {
if ( ! ( obj instanceof SequenomVariantInfo ) ) {
return 1;
}
return loc.compareTo(((SequenomVariantInfo) obj).getLocation());
}
}