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Potential bug fix for bad references where some codons may have Ns 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@4075 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
depristo 2010-08-21 12:09:33 +00:00
parent 121b4f23b6
commit b6989289fc
3 changed files with 44 additions and 40 deletions
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5
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/AminoAcid.java
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@ -82,6 +82,11 @@ public class AminoAcid {
return "*".equals(getLetter());
}
/** Returns true if the amino acid is really just a stop codon. */
public boolean isUnknown() {
return "X".equals(getLetter());
}
public String toString() {
return name;
}

16
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/AminoAcidTable.java
View File

@ -34,6 +34,7 @@ import java.util.HashMap;
public class AminoAcidTable {
protected static final AminoAcid UNKNOWN = new AminoAcid("X" , "Unknown", "Unk");
protected static final AminoAcid ISOLEUCINE = new AminoAcid("I" , "Isoleucine", "Ile");
protected static final AminoAcid LEUCINE = new AminoAcid("L" , "Leucine", "Leu");
protected static final AminoAcid VALINE = new AminoAcid("V" , "Valine", "Val");
@ -177,24 +178,17 @@ public class AminoAcidTable {
mitochondrialAminoAcidTable.put("TGA", TRYPTOPHAN);
}
/**
* Returns the amino acid encoded by the given codon in a eukaryotic genome.
*
* @param codon The 3-letter mRNA nucleotide codon 5' to 3'. Expects T's instead of U's. Not case sensitive.
*
* @return The amino acid matching the given codon.
* @return The amino acid matching the given codon, or the UNKNOWN amino acid if the codon string doesn't match anything
*/
public static AminoAcid getEukaryoticAA(String codon) {
codon = codon.toUpperCase();
final AminoAcid aa = aminoAcidTable.get(codon);
if(aa == null) {
throw new IllegalArgumentException("Invalid codon: " + codon);
} else {
return aa;
}
return aa == null ? UNKNOWN : aa;
}
@ -204,13 +198,13 @@ public class AminoAcidTable {
* @param codon The 3-letter mRNA nucleotide codon 5' to 3'. Expects T's instead of U's. Not case sensitive.
* @param isFirstCodon If this is the 1st codon in the gene, then "ATT" encodes Methyonine
*
* @return The amino acid matching the given codon in mitochondrial genes.
* @return The amino acid matching the given codon in mitochondrial genes, or the UNKNOWN amino acid if the codon string doesn't match anything
*/
public static AminoAcid getMitochondrialAA(String codon, boolean isFirstCodon) {
codon = codon.toUpperCase();
final AminoAcid aa = mitochondrialAminoAcidTable.get(codon);
if(aa == null) {
throw new IllegalArgumentException("Invalid codon: " + codon);
return UNKNOWN;
} else if(isFirstCodon && codon.equals("ATT")) {
return METHIONINE; //special case - 'ATT' in the first codon of a mitochondrial gene codes for methionine instead of isoleucine
} else {

63
java/src/org/broadinstitute/sting/playground/gatk/walkers/annotator/TranscriptToInfo.java
View File

@ -620,10 +620,10 @@ public class TranscriptToInfo extends RodWalker<TreeMap<String, String>, TreeMap
//check for bad bases
if( (utr5NucBuffer_5to3[0] != 0 && !BaseUtils.isRegularBase(utr5NucBuffer_5to3[0])) ||
(utr5NucBuffer_5to3[1] != 0 && !BaseUtils.isRegularBase(utr5NucBuffer_5to3[1])) ||
(utr5NucBuffer_5to3[2] != 0 && !BaseUtils.isRegularBase(utr5NucBuffer_5to3[2])) ||
(utr5NucBuffer_5to3[3] != 0 && !BaseUtils.isRegularBase(utr5NucBuffer_5to3[3])) ||
(utr5NucBuffer_5to3[4] != 0 && !BaseUtils.isRegularBase(utr5NucBuffer_5to3[4])))
(utr5NucBuffer_5to3[1] != 0 && !BaseUtils.isRegularBase(utr5NucBuffer_5to3[1])) ||
(utr5NucBuffer_5to3[2] != 0 && !BaseUtils.isRegularBase(utr5NucBuffer_5to3[2])) ||
(utr5NucBuffer_5to3[3] != 0 && !BaseUtils.isRegularBase(utr5NucBuffer_5to3[3])) ||
(utr5NucBuffer_5to3[4] != 0 && !BaseUtils.isRegularBase(utr5NucBuffer_5to3[4])))
{
logger.debug("Skipping current position [" + parsedTranscriptRod.txChrom + ":" +txCoord_5to3 + "] in transcript " + parsedTranscriptRod.geneNames.toString() +". utr5NucBuffer_5to3 contains irregular base:" + utr5NucBuffer_5to3[0] + utr5NucBuffer_5to3[1] + utr5NucBuffer_5to3[2] + utr5NucBuffer_5to3[3] + utr5NucBuffer_5to3[4]);// +". Transcript is: " + parsedTranscriptRod);
++skippedPositionsCounter;
@ -735,8 +735,8 @@ public class TranscriptToInfo extends RodWalker<TreeMap<String, String>, TreeMap
//check for +1 (eg. addition of new ATG uORF) and -1 (eg. disruption of existing ATG uORF)
String uORFChangeStr = null;
if( (refCodon1.equals("ATG") && !varCodon1.equals("ATG")) ||
(refCodon2.equals("ATG") && !varCodon2.equals("ATG")) ||
(refCodon3.equals("ATG") && !varCodon3.equals("ATG")))
(refCodon2.equals("ATG") && !varCodon2.equals("ATG")) ||
(refCodon3.equals("ATG") && !varCodon3.equals("ATG")))
{
uORFChangeStr = "-1";
}
@ -753,17 +753,22 @@ public class TranscriptToInfo extends RodWalker<TreeMap<String, String>, TreeMap
else if(positionType == PositionType.CDS)
{
final String referenceCodon = Character.toString(currentCodon_5to3[0]) + Character.toString(currentCodon_5to3[1]) + currentCodon_5to3[2];
outputLineFields.put(OUTPUT_FRAME, Integer.toString(frame) );
outputLineFields.put(OUTPUT_CODON_NUMBER, Integer.toString(codonCount_from5) );
final String variantCodon = Character.toString(currentCodon_5to3[0]) + Character.toString(currentCodon_5to3[1]) + currentCodon_5to3[2];
final AminoAcid refAA = isMitochondrialTranscript ? AminoAcidTable.getMitochondrialAA( referenceCodon, codonCount_from5 == 1 ) : AminoAcidTable.getEukaryoticAA( referenceCodon ) ;
final AminoAcid variantAA = isMitochondrialTranscript ? AminoAcidTable.getMitochondrialAA( variantCodon, codonCount_from5 == 1 ) : AminoAcidTable.getEukaryoticAA( variantCodon ) ;
if ( refAA.isUnknown() || variantAA.isUnknown() ) {
logger.warn("Illegal amino acid detected: refCodon=" + referenceCodon + " altCodon=" + variantCodon);
}
outputLineFields.put(OUTPUT_FRAME, Integer.toString(frame) );
outputLineFields.put(OUTPUT_CODON_NUMBER, Integer.toString(codonCount_from5) );
outputLineFields.put(OUTPUT_REFERENCE_CODON, referenceCodon );
outputLineFields.put(OUTPUT_REFERENCE_AA, refAA.getCode());
final char temp = currentCodon_5to3[frame];
currentCodon_5to3[frame] = haplotypeAlternate;
final String variantCodon = Character.toString(currentCodon_5to3[0]) + Character.toString(currentCodon_5to3[1]) + currentCodon_5to3[2];
final AminoAcid variantAA = isMitochondrialTranscript ? AminoAcidTable.getMitochondrialAA( variantCodon, codonCount_from5 == 1 ) : AminoAcidTable.getEukaryoticAA( variantCodon ) ;
outputLineFields.put(OUTPUT_VARIANT_CODON, variantCodon );
outputLineFields.put(OUTPUT_VARIANT_AA, variantAA.getCode());
@ -915,23 +920,23 @@ public class TranscriptToInfo extends RodWalker<TreeMap<String, String>, TreeMap
long key;
final char lastChromChar = txChrom.charAt(txChrom.length() -1);
switch( Character.toLowerCase(lastChromChar) ) {
case 'm':
case 't': // for hg19 or b36
key = 0;
break;
case 'x':
key = 23;
break;
case 'y':
key = 24;
break;
default:
if( txChrom.startsWith("chr") ) {
key = Integer.parseInt(txChrom.substring(3));
} else {
key = Integer.parseInt(txChrom);
}
break;
case 'm':
case 't': // for hg19 or b36
key = 0;
break;
case 'x':
key = 23;
break;
case 'y':
key = 24;
break;
default:
if( txChrom.startsWith("chr") ) {
key = Integer.parseInt(txChrom.substring(3));
} else {
key = Integer.parseInt(txChrom);
}
break;
}
key++; //shift so there's no zero (otherwise, multiplication is screwed up in the next step)
@ -1108,8 +1113,8 @@ public class TranscriptToInfo extends RodWalker<TreeMap<String, String>, TreeMap
//exonFrames = new int[exonCount];
for(int i = 0; i < exonCount; i++) {
exonStarts[i] = Integer.parseInt(exonStartStrs[i]);
exonEnds[i] = Integer.parseInt(exonEndStrs[i]);
//exonFrames[i] = Integer.parseInt(exonFrameStrs[i]);
exonEnds[i] = Integer.parseInt(exonEndStrs[i]);
//exonFrames[i] = Integer.parseInt(exonFrameStrs[i]);
}
}