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Added MNP annotation of the number of AA changes occuring in the SAME RefSeq entry (numAAchanges), and if this number is > 1 for any of the alt alleles (alleleHasMultAAchanges) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4746 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
fromer 2010-11-29 21:24:30 +00:00
parent 222cd42ceb
commit 727dac7b7a
1 changed files with 42 additions and 7 deletions
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49
java/src/org/broadinstitute/sting/gatk/walkers/phasing/AnnotateMNPsWalker.java
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@ -98,6 +98,8 @@ public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
protected final static String REFSEQ_PROTEIN_COORD_DESCRIPTION = "proteinCoordStr";
protected final static String REFSEQ_CODING_ANNOTATIONS = "codingVariants";
protected final static String REFSEQ_NUM_AA_CHANGES = "numAAchanges";
protected final static String REFSEQ_HAS_MULT_AA_CHANGES = "alleleHasMultAAchanges";
public void initialize() {
rodNames = new LinkedList<String>();
@ -230,7 +232,9 @@ public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
RefSeqFeatureList feature = nameToFeatureEntry.getValue();
CodonAnnotationsForAltAlleles codonAnnotationsForAlleles = new CodonAnnotationsForAltAlleles(vc, feature);
annotations.put(kb.getKey(REFSEQ_CODING_ANNOTATIONS), codonAnnotationsForAlleles.toString());
annotations.put(kb.getKey(REFSEQ_CODING_ANNOTATIONS), codonAnnotationsForAlleles.getCodonAnnotationsString());
annotations.put(kb.getKey(REFSEQ_NUM_AA_CHANGES), codonAnnotationsForAlleles.getNumAAchangesString());
annotations.put(kb.getKey(REFSEQ_HAS_MULT_AA_CHANGES), codonAnnotationsForAlleles.hasAlleleWithMultipleAAchanges);
annotations.put(kb.getKey(REFSEQ_NAME), featureName);
annotations.put(kb.getKey(REFSEQ_NAME2), feature.name2);
annotations.put(kb.getKey(REFSEQ_POSITION_TYPE), REFSEQ_CDS);
@ -438,10 +442,18 @@ public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
private final static String CODON_ANNOTATION_DELIM = ",";
private List<SingleCodonAnnotationsForAlleles> alleleAnnotations;
private int[] alleleToNumAAchanges;
private boolean hasAlleleWithMultipleAAchanges;
public CodonAnnotationsForAltAlleles(VariantContext vc, RefSeqFeatureList feature) {
this.alleleAnnotations = new LinkedList<SingleCodonAnnotationsForAlleles>();
Set<Allele> altAlleles = vc.getAlternateAlleles();
int numAltAlleles = altAlleles.size();
this.alleleToNumAAchanges = new int[numAltAlleles];
for (int i = 0; i < numAltAlleles; i++)
this.alleleToNumAAchanges[i] = 0;
int MNPstart = vc.getStart();
int MNPstop = vc.getEnd();
int MNPlength = MNPstop - MNPstart + 1;
@ -462,12 +474,21 @@ public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
CodingRefSeqFeature firstFeatureForCodon = feature.refSeqFeatures[indices.get(0)];
String refCodon = firstFeatureForCodon.referenceCodon;
SingleCodonAnnotationsForAlleles codonAnnotation = new SingleCodonAnnotationsForAlleles(codonIndex, vc.getAlternateAlleles(), MNPlength, refCodon, firstFeatureForCodon, indices, feature);
SingleCodonAnnotationsForAlleles codonAnnotation = new SingleCodonAnnotationsForAlleles(codonIndex, altAlleles, MNPlength, refCodon, firstFeatureForCodon, indices, feature);
alleleAnnotations.add(codonAnnotation);
// From a single codon, summarize the data for ALL alleles:
for (int i = 0; i < numAltAlleles; i++) {
if (codonAnnotation.annotationsForAlleles[i].codonFunc.changesAA) {
alleleToNumAAchanges[i]++;
if (alleleToNumAAchanges[i] > 1)
this.hasAlleleWithMultipleAAchanges = true;
}
}
}
}
public String toString() {
public String getCodonAnnotationsString() {
StringBuilder sb = new StringBuilder();
int index = 0;
@ -480,6 +501,18 @@ public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
return sb.toString();
}
public String getNumAAchangesString() {
StringBuilder sb = new StringBuilder();
for (int index = 0; index < alleleToNumAAchanges.length; index++) {
sb.append(alleleToNumAAchanges[index]);
if (index < alleleToNumAAchanges.length - 1)
sb.append(SingleCodonAnnotationsForAlleles.ALLELE_ANNOTATION_DELIM);
}
return sb.toString();
}
}
private static class SingleCodonAnnotationsForAlleles {
@ -494,7 +527,7 @@ public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
private String refCodon;
private String refAA;
private List<SingleCodonAnnotationsForAllele> annotationsForAlleles;
private SingleCodonAnnotationsForAllele[] annotationsForAlleles;
public SingleCodonAnnotationsForAlleles(int codonIndex, Collection<Allele> altAlleles, int MNPlength, String refCodon, CodingRefSeqFeature firstFeatureForCodon, List<Integer> indices, RefSeqFeatureList feature) {
if (refCodon.length() != CodonAnnotationsForAltAlleles.NUM_CODON_INDICES)
@ -507,8 +540,9 @@ public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
this.codonIndex = codonIndex;
this.refCodon = refCodon;
this.refAA = refAA.getCode();
this.annotationsForAlleles = new LinkedList<SingleCodonAnnotationsForAllele>();
this.annotationsForAlleles = new SingleCodonAnnotationsForAllele[altAlleles.size()];
int altInd = 0;
for (Allele altAllele : altAlleles) {
if (altAllele.length() != MNPlength)
throw new ReviewedStingException("length(altAllele) != length(MNP)");
@ -540,7 +574,8 @@ public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
String variantCodon = new String(ByteArrayToPrimitive(variantCodonArr)).toUpperCase();
SingleCodonAnnotationsForAllele alleleAnnotation = new SingleCodonAnnotationsForAllele(variantCodon, refCodon, refAA, codonIndex);
annotationsForAlleles.add(alleleAnnotation);
annotationsForAlleles[altInd] = alleleAnnotation;
altInd++;
}
}
@ -554,7 +589,7 @@ public class AnnotateMNPsWalker extends RodWalker<Integer, Integer> {
int index = 0;
for (SingleCodonAnnotationsForAllele annotation : annotationsForAlleles) {
sb.append(annotation);
if (index < annotationsForAlleles.size() - 1)
if (index < annotationsForAlleles.length - 1)
sb.append(ALLELE_ANNOTATION_DELIM);
index++;
}