236 lines
8.8 KiB
Java
236 lines
8.8 KiB
Java
package org.broadinstitute.sting.gatk.refdata;
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import edu.mit.broad.picard.util.SequenceUtil;
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import java.util.*;
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import org.broadinstitute.sting.gatk.refdata.ReferenceOrderedDatum;
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import org.broadinstitute.sting.utils.GenomeLoc;
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import org.broadinstitute.sting.utils.Utils;
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import org.broadinstitute.sting.gatk.refdata.AllelicVariant;
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/**
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* Example format:
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* 585 chr1 433 433 rs56289060 0 + - - -/C genomic insertion unknown 0 0 unknown between 1
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* 585 chr1 491 492 rs55998931 0 + C C C/T genomic single unknown 0 0 unknown exact 1
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*
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* User: mdepristo
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* Date: Feb 27, 2009
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* Time: 10:47:14 AM
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* To change this template use File | Settings | File Templates.
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*/
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public class rodDbSNP extends BasicReferenceOrderedDatum implements AllelicVariant {
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public GenomeLoc loc; // genome location of SNP
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// Reference sequence chromosome or scaffold
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// Start and stop positions in chrom
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public String name; // Reference SNP identifier or Affy SNP name
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public String strand; // Which DNA strand contains the observed alleles
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public String refBases; // the reference base according to NCBI, in the dbSNP file
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public String observed; // The sequences of the observed alleles from rs-fasta files
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public String molType; // Sample type from exemplar ss
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public String varType; // The class of variant (simple, insertion, deletion, range, etc.)
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// Can be 'unknown','single','in-del','het','microsatellite','named','mixed','mnp','insertion','deletion'
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public String validationStatus; // The validation status of the SNP
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// one of set('unknown','by-cluster','by-frequency','by-submitter','by-2hit-2allele','by-hapmap')
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public double avHet; // The average heterozygosity from all observations
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public double avHetSE; // The Standard Error for the average heterozygosity
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public String func; // The functional category of the SNP (coding-synon, coding-nonsynon, intron, etc.)
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// set('unknown','coding-synon','intron','cds-reference','near-gene-3','near-gene-5',
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// 'nonsense','missense','frameshift','untranslated-3','untranslated-5','splice-3','splice-5')
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public String locType; // How the variant affects the reference sequence
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// enum('range','exact','between','rangeInsertion','rangeSubstitution','rangeDeletion')
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public int weight; // The quality of the alignment
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// ----------------------------------------------------------------------
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//
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// Constructors
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//
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// ----------------------------------------------------------------------
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public rodDbSNP(final String name) {
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super(name);
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}
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// ----------------------------------------------------------------------
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//
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// manipulating the SNP information
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//
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// ----------------------------------------------------------------------
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public GenomeLoc getLocation() { return loc; }
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public boolean onFwdStrand() {
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return strand.equals("+");
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}
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/** Returns bases in the reference allele as a String. String can be empty (as in insertion into
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* the reference), can contain a single character (as in SNP or one-base deletion), or multiple characters
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* (for longer indels).
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*
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* @return reference allele, forward strand
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*/
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public String getRefBasesFWD() {
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if ( onFwdStrand() )
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return refBases;
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else
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return SequenceUtil.reverseComplement(refBases);
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}
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/**
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* Returns reference (major) allele base for a SNP variant as a character; should throw IllegalStateException
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* if variant is not a SNP.
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*
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* @return reference base on the forward strand
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*/
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public char getRefSnpFWD() throws IllegalStateException {
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if ( isIndel() ) throw new IllegalStateException("Variant is not a SNP");
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if ( onFwdStrand() ) return refBases.charAt(0);
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else return SequenceUtil.reverseComplement(refBases).charAt(0);
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}
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public List<String> getAllelesFWD() {
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List<String> alleles = null;
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if ( onFwdStrand() )
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alleles = Arrays.asList(observed.split("/"));
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else
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alleles = Arrays.asList(SequenceUtil.reverseComplement(observed).split("/"));
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//System.out.printf("getAlleles %s on %s %b => %s %n", observed, strand, onFwdStrand(), Utils.join("/", alleles));
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return alleles;
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}
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public String getAllelesFWDString() {
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return Utils.join("/", getAllelesFWD());
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}
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// ----------------------------------------------------------------------
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//
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// What kind of variant are we?
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//
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// ----------------------------------------------------------------------
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public boolean isSNP() { return varType.contains("single"); }
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public boolean isInsertion() { return varType.contains("insertion"); }
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public boolean isDeletion() { return varType.contains("deletion"); }
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public boolean isIndel() { return isInsertion() || isDeletion() || varType.contains("in-del"); }
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public boolean isReference() { return false; } // snp locations are never "reference", there's always a snp!!
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public boolean isHapmap() { return validationStatus.contains("by-hapmap"); }
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public boolean is2Hit2Allele() { return validationStatus.contains("by-2hit-2allele"); }
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// ----------------------------------------------------------------------
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//
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// formatting
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//
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// ----------------------------------------------------------------------
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public String toString() {
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return String.format("%s\t%d\t%d\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%f\t%f\t%s\t%s\t%d",
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getLocation().getContig(), getLocation().getStart(), getLocation().getStop(),
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name, strand, refBases, observed, molType,
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varType, validationStatus, avHet, avHetSE, func, locType, weight );
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}
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public String toSimpleString() {
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return String.format("%s:%s:%s", name, observed, strand);
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}
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public String toMediumString() {
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String s = String.format("%s:%s:%s", getLocation().toString(), name, getAllelesFWDString());
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if ( isSNP() ) s += ":SNP";
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if ( isIndel() ) s += ":Indel";
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if ( isHapmap() ) s += ":Hapmap";
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if ( is2Hit2Allele() ) s += ":2Hit";
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return s;
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}
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public String repl() {
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return String.format("%d\t%s\t%d\t%d\t%s\t0\t%s\t%s\t%s\t%s\t%s\t%s\t%s\t%f\t%f\t%s\t%s\t%d",
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585, getLocation().getContig(), getLocation().getStart()-1, getLocation().getStop()-1,
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name, strand, refBases, refBases, observed, molType,
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varType, validationStatus, avHet, avHetSE, func, locType, weight );
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}
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public boolean parseLine(final Object header, final String[] parts) {
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try {
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String contig = parts[1];
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long start = Long.parseLong(parts[2]) + 1; // The final is 0 based
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long stop = Long.parseLong(parts[3]) + 1; // The final is 0 based
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loc = new GenomeLoc(contig, start, stop);
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name = parts[4];
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refBases = parts[5];
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strand = parts[6];
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observed = parts[9];
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molType = parts[10];
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varType = parts[11];
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validationStatus = parts[12];
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avHet = Double.parseDouble(parts[13]);
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avHetSE = Double.parseDouble(parts[14]);
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func = parts[15];
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locType = parts[16];
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weight = Integer.parseInt(parts[17]);
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return true;
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} catch ( RuntimeException e ) {
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System.out.printf(" Exception caught during parsing GFFLine %s%n", Utils.join(" <=> ", parts));
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throw e;
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}
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}
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@Override
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public String getAltBasesFWD() {
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// TODO Auto-generated method stub
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return null;
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}
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@Override
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public char getAltSnpFWD() throws IllegalStateException {
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// TODO Auto-generated method stub
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return 0;
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}
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@Override
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public double getConsensusConfidence() {
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// TODO Auto-generated method stub
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return 0;
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}
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@Override
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public List<String> getGenotype() throws IllegalStateException {
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// TODO Auto-generated method stub
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return null;
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}
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@Override
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public double getMAF() {
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// TODO Auto-generated method stub
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return 0;
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}
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@Override
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public int getPloidy() throws IllegalStateException {
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// TODO Auto-generated method stub
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return 0;
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}
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@Override
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public double getVariationConfidence() {
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// TODO Auto-generated method stub
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return 0;
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}
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@Override
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public boolean isGenotype() {
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// TODO Auto-generated method stub
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return false;
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}
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@Override
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public boolean isBiallelic() {
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// TODO Auto-generated method stub
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return observed.indexOf('/')==observed.lastIndexOf('/');
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}
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}
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