1st attempt to implement extra columns
git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@3249 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
weisburd
parent
a72a5a7b1a
commit
10bcd72593
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@ -80,7 +80,7 @@ public class TranscriptToInfo extends RodWalker<Integer, Integer>
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public static final String OUTPUT_MRNA_COORD = "mrnaCoord"; //1-based offset within the transcript
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public static final String OUTPUT_CODING_COORD = "codingCoord"; //1-based offset within the cds region
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public static final String OUTPUT_SPLICE_DISTANCE = "minSpliceDistance"; //eg. 40
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public static final String OUTPUT_SPLICE_DISTANCE = "spliceDist"; //eg. integer, bp to nearest exon/intron boundary
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public static final String OUTPUT_CODON_NUMBER = "codonCoord"; //eg. 20
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public static final String OUTPUT_REFERENCE_CODON = "referenceCodon";
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@ -90,9 +90,14 @@ public class TranscriptToInfo extends RodWalker<Integer, Integer>
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public static final String OUTPUT_CHANGES_AMINO_ACID = "changesAA"; //eg. true
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public static final String OUTPUT_CODING_COORD_STR = "coding_coord_str";
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public static final String OUTPUT_PROTEIN_COORD_STR = "protein_coord_str";
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public static final String OUTPUT_INTRON_COORD_STR = "intron_coord_str";
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public static final String OUTPUT_CODING_COORD_STR = "codingCoordStr";
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public static final String OUTPUT_PROTEIN_COORD_STR = "proteinCoordStr";
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//public static final String OUTPUT_INTRON_COORD_STR = "intron_coord_str";
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public static final String OUTPUT_SPLICE_INFO = "spliceInfo"; //(eg "splice-donor -4", or "splice-acceptor 3") for the 10bp surrounding each exon/intron boundary
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public static final String OUTPUT_UORF_CHANGE = "uorfChange"; // (eg +1 or -1, indicating the addition or interruption of an ATG trinucleotide in the annotated utr5)
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public static final String[] OUTPUT_COLUMN_NAMES = new String[] {
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OUTPUT_SORT_KEY,
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@ -122,9 +127,10 @@ public class TranscriptToInfo extends RodWalker<Integer, Integer>
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OUTPUT_CODING_COORD_STR,
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OUTPUT_PROTEIN_COORD_STR,
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OUTPUT_INTRON_COORD_STR,
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OUTPUT_IN_CODING_REGION,
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OUTPUT_SPLICE_INFO,
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OUTPUT_UORF_CHANGE,
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};
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@ -258,16 +264,21 @@ public class TranscriptToInfo extends RodWalker<Integer, Integer>
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/**
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* Computes the distance to the nearest splice-site.
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* Returns 1 when down-stream of splice-juction, -1 when upstream
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* The returned value is negative its on the 5' side (eg. upstream) of the juntion, and
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* positive if its on the 3' side.
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*/
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public int distanceToSpliceSite(final long genomPosition) {
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public int computeDistanceToNearestSpliceSite(final long genomPosition) {
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int prevDistance = Integer.MAX_VALUE;
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int curDistance;
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for(int i = 0; i < exonStarts.length; i++) {
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final long curStart = exonStarts[i];
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curDistance = (int) (curStart-genomPosition);
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int curDistance = (int) (curStart-genomPosition);
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if(genomPosition < curStart) {
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return Math.min(prevDistance, curDistance);
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//position is within the current intron
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if(prevDistance < curDistance) {
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return positiveStrand ? prevDistance : -prevDistance;
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} else {
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return positiveStrand ? -curDistance : curDistance;
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}
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} else {
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prevDistance = (int) (genomPosition - curStart) + 1;
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}
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@ -275,13 +286,21 @@ public class TranscriptToInfo extends RodWalker<Integer, Integer>
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final long curStop = exonEnds[i];
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curDistance = (int) (curStop-genomPosition) + 1;
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if(genomPosition <= curStop) {
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return Math.min(prevDistance, curDistance);
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//position is within an exon
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if(prevDistance < curDistance) {
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return positiveStrand ? prevDistance : -prevDistance;
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} else {
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return positiveStrand ? -curDistance : curDistance;
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}
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} else {
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prevDistance = (int) (genomPosition - curStop);
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}
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}
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return prevDistance; //out of exons. return genomPosition-curStop
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throw new IllegalArgumentException("Genomic position: [" + genomPosition +"] not found within transcript: " + this +". " +
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"This method should not have been called for this position. NOTE: this method assumes that all transcripts start " +
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"with an exon and end with an exon (rather than an intron). Is this wrong?");
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//return prevDistance; //out of exons. return genomPosition-curStop
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}
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@ -298,6 +317,66 @@ public class TranscriptToInfo extends RodWalker<Integer, Integer>
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return rod.toString();
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}
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/**
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* Computes the coding coord of the 1st nucleotide in the transcript.
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* If the 1st nucleotide is in the 5'utr, the returned value will be negative.
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* Otherwise (if the 1st nucleotide is CDS), the returned value is 1.
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*/
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public int computeInitialCodingCoord() {
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if(!isProteinCodingTranscript()) {
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throw new StingException("This method should only be called for protein-coding transcripts");
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}
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if(positiveStrand)
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{
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if( cdsStart == exonStarts[0] ) {
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//the 1st nucleotide of the transcript is CDS.
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return 1;
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}
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int result = 0;
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for(int i = 0; i < exonStarts.length; i++)
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{
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final long exonStart = exonStarts[i];
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final long exonEnd = exonEnds[i];
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if(cdsStart <= exonEnd) { //eg. exonEnd is now on the 3' side of cdsStart
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//this means cdsStart is within the current exon
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result += (cdsStart - exonStart) + 1;
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break;
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} else {
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//cdsStart is downstream of the current exon
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result += (exonEnd - exonStart) + 1;
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}
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}
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return -result; //negate because 5' UTR coding coord is negative
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}
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else //(negative strand)
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{
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final long cdsStart_5prime = cdsEnd;
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if(cdsStart_5prime == exonEnds[exonEnds.length - 1]) {
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//the 1st nucleotide of the transcript is CDS.
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return 1;
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}
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int result = 0;
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for(int i = exonEnds.length - 1; i >= 0; i--)
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{
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final long exonStart = exonEnds[i]; //when its the negative strand, the 5' coord of the 1st exon is exonEnds[i]
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final long exonEnd = exonStarts[i];
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if( exonEnd <= cdsStart_5prime ) { //eg. exonEnd is now on the 3' side of cdsStart
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//this means cdsStart is within the current exon
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result += -(cdsStart_5prime - exonStart) + 1;
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break;
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} else {
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//cdsStart is downstream of the current exon
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result += -(exonEnd - exonStart) + 1;
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}
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}
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return -result; //negate because 5' UTR coding coord is negative
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}
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}
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}
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@ -362,7 +441,7 @@ public class TranscriptToInfo extends RodWalker<Integer, Integer>
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return 0;
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Collection<RODRecordList> rods = tracker.getBoundRodTracks();
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final Collection<RODRecordList> rods = tracker.getBoundRodTracks();
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if(rods.size() == 0) {
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//if there's nothing overlapping this locus, skip it.
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return 0;
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@ -378,7 +457,7 @@ public class TranscriptToInfo extends RodWalker<Integer, Integer>
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throw new RuntimeException("The 'refgene' -B arg must have the type: 'AnnotatorInputTable'.");
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}
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AnnotatorROD refGeneRod = (AnnotatorROD) refGeneRodObject;
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final AnnotatorROD refGeneRod = (AnnotatorROD) refGeneRodObject;
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RefGeneTranscriptRecord parsedRefGeneRod = (RefGeneTranscriptRecord) refGeneRod.getTemporaryAttribute("parsedRefGeneRod");
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if( parsedRefGeneRod == null ) {
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parsedRefGeneRod = new RefGeneTranscriptRecord(refGeneRod);
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@ -429,30 +508,30 @@ public class TranscriptToInfo extends RodWalker<Integer, Integer>
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if(isProteinCodingTranscript && parsedRefGeneRod.cdsSequence.length() % 3 != 0) {
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System.err.println("WARNING: The following record has " + parsedRefGeneRod.cdsSequence.length() + " nucleotides in its CDS region, which is not divisible by 3. Skipping... \n" + parsedRefGeneRod.toString());
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//TODO figure out why all CDS lengths aren't in multiples of 3 nucleotides - Sarah says its ok to thow these out.
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//discard transcripts where CDS length is not a multiple of 3
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return;
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}
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//here, 5' and 3' are according to the DNA (not on the RNA)
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int frame = 0; //the frame of the current position
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int txOffset_from5 = 1; //goes from txStart 5' to txEnd 3' for both + and - strand
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int proteinOffset_from5 = 1; //goes from cdsStart 5' to cdsEnd 3' for both + and - strand
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int codonOffset_from5 = 0; //goes from cdsStart 5' to cdsEnd 3' for both + and - strand - counts the number of codons (this count is 1-based even though its set to 0 here.)
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char[] currentCodon_5to3 = null; //holds the current RNA codon - 5' to 3'
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final long txStart_5prime = positiveStrand ? parsedRefGeneRod.txStart : parsedRefGeneRod.txEnd; //1-based, inclusive
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final long txEnd_3prime = positiveStrand ? parsedRefGeneRod.txEnd : parsedRefGeneRod.txStart; //1-based, inclusive
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final int increment_5to3 = positiveStrand ? 1 : -1;
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final int increment_5to3 = positiveStrand ? 1 : -1; //whether to increment or decrement
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final int strandSign = increment_5to3; //alias
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final long cdsStart_5prime = positiveStrand ? parsedRefGeneRod.cdsStart : parsedRefGeneRod.cdsEnd; //1-based, inclusive
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final long cdsEnd_3prime = positiveStrand ? parsedRefGeneRod.cdsEnd : parsedRefGeneRod.cdsStart ; //1-based, inclusive
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//compute chromosome key (later used to sort the output file)
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int frame = 0; //the frame of the current position
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int txOffset_from5 = 1; //goes from txStart 5' to txEnd 3' for both + and - strand
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int codonCount_from5 = 0; //goes from cdsStart 5' to cdsEnd 3' for both + and - strand - counts the number of codons (this count is 1-based even though its set to 0 here.)
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int codingCoord_from5 = isProteinCodingTranscript ? parsedRefGeneRod.computeInitialCodingCoord() : 0; //goes from cdsStart 5' to cdsEnd 3' for both + and - strand
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boolean mitochondrial = false;
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//compute chromosome sort key (this becomes the 1st column in the file and is later used to sort the output file using the GNU command-line sort utility)
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long chromKey;
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final char lastChromChar = parsedRefGeneRod.txChrom.charAt(parsedRefGeneRod.txChrom.length() -1);
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switch( Character.toLowerCase(lastChromChar) ) {
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@ -474,6 +553,7 @@ public class TranscriptToInfo extends RodWalker<Integer, Integer>
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chromKey++; //shift so there's no zero (otherwise, multiplication is screwed up in the next step)
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chromKey *= 100000000000L;
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PositionType positionType = null;
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for(long txCoord_5to3 = txStart_5prime; txCoord_5to3 != txEnd_3prime + increment_5to3; txCoord_5to3 += increment_5to3)
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{
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@ -483,18 +563,28 @@ public class TranscriptToInfo extends RodWalker<Integer, Integer>
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//whether the current txCoord_5to3 is within an exon
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final boolean isWithinExon = parsedRefGeneRod.isWithinExon(txCoord_5to3); //TODO if necessary, this can be sped up by keeping track of current exon/intron
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final int distanceToNearestSpliceSite = parsedRefGeneRod.computeDistanceToNearestSpliceSite(txCoord_5to3);
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//figure out what region the current position is in.
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PositionType positionType;
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if(isProteinCodingTranscript)
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{
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if(isWithinExon)
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{
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if( strandSign*(txCoord_5to3 - cdsStart_5prime) < 0 ) {
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//update positionType (and codingCoord_from5 if needed)
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if( strandSign*(txCoord_5to3 - cdsStart_5prime) < 0 ) { //multiplying by strandSign is like doing absolute value.
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positionType = PositionType.utr5;
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} else if( strandSign*(txCoord_5to3 - cdsEnd_3prime) > 0 ) {
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positionType = PositionType.utr3;
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} else if( strandSign*(txCoord_5to3 - cdsEnd_3prime) > 0 ) { //multiplying by strandSign is like doing absolute value.
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if(positionType != PositionType.utr3) {
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//if we're transitioning from CDS to utr3, reset the coding coord to 1.
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codingCoord_from5 = 1; //reset the coding coord for utr3
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positionType = PositionType.utr3;
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}
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} else {
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positionType = PositionType.CDS;
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if(positionType != PositionType.CDS) {
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//if we're transitioning from utr5 to CDS, reset the coding coord from -1 to 1.
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codingCoord_from5 = 1;
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positionType = PositionType.CDS;
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}
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}
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} else {
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positionType = PositionType.intron;
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@ -514,11 +604,11 @@ public class TranscriptToInfo extends RodWalker<Integer, Integer>
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currentCodon_5to3 = new char[3];
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}
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codonOffset_from5++;
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codonCount_from5++;
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currentCodon_5to3[0] = parsedRefGeneRod.cdsSequence.charAt( proteinOffset_from5 - 1 ); //subtract 1 to go to zero-based coords
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currentCodon_5to3[1] = parsedRefGeneRod.cdsSequence.charAt( proteinOffset_from5 );
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currentCodon_5to3[2] = parsedRefGeneRod.cdsSequence.charAt( proteinOffset_from5 + 1);
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currentCodon_5to3[0] = parsedRefGeneRod.cdsSequence.charAt( codingCoord_from5 - 1 ); //subtract 1 to go to zero-based coords
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currentCodon_5to3[1] = parsedRefGeneRod.cdsSequence.charAt( codingCoord_from5 );
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currentCodon_5to3[2] = parsedRefGeneRod.cdsSequence.charAt( codingCoord_from5 + 1);
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if(!positiveStrand) {
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currentCodon_5to3[0] = BaseUtils.simpleComplement(currentCodon_5to3[0]);
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@ -527,9 +617,6 @@ public class TranscriptToInfo extends RodWalker<Integer, Integer>
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}
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}
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final String distanceToSpliceSiteString = Integer.toString(parsedRefGeneRod.distanceToSpliceSite(txCoord_5to3));
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for(final char haplotypeAlternate : ALLELES )
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{
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final LinkedHashMap<String, String> outputLineFields = new LinkedHashMap<String, String>();
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@ -545,55 +632,104 @@ public class TranscriptToInfo extends RodWalker<Integer, Integer>
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outputLineFields.put(OUTPUT_POSITION_TYPE, positionType.toString() );
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outputLineFields.put(OUTPUT_MRNA_COORD, Integer.toString(txOffset_from5) );
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outputLineFields.put(OUTPUT_SPLICE_DISTANCE, distanceToSpliceSiteString );
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outputLineFields.put(OUTPUT_SPLICE_DISTANCE, Integer.toString(distanceToNearestSpliceSite) );
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//comppute OUTPUT_SPLICE_INFO
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final String spliceInfoString;
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if(Math.abs(distanceToNearestSpliceSite) <= 10) {
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if(distanceToNearestSpliceSite < 0) {
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//is on the 5' side of the splice junction
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if(isWithinExon) {
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spliceInfoString = "splice-donor " + distanceToNearestSpliceSite;
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} else {
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spliceInfoString = "splice-acceptor " + distanceToNearestSpliceSite;
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}
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} else {
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if(isWithinExon) {
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spliceInfoString = "splice-acceptor " + distanceToNearestSpliceSite;
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} else {
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spliceInfoString = "splice-donor " + distanceToNearestSpliceSite;
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}
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}
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outputLineFields.put(OUTPUT_SPLICE_INFO, spliceInfoString);
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}
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if(isProteinCodingTranscript)
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{
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outputLineFields.put(OUTPUT_IN_CODING_REGION, Boolean.toString(positionType == PositionType.CDS) );
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if(isWithinExon) {
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outputLineFields.put(OUTPUT_CODING_COORD, Integer.toString(proteinOffset_from5) );
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if(positionType == PositionType.CDS) {
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if(isWithinExon)
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{
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if(positionType == PositionType.utr5)
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{
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/*
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if(THIS IS A uORF)
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outputLineFields.put(OUTPUT_UORF_CHANGE, "TODO" ); //TODO put this here
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*/
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}
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else if(positionType == PositionType.CDS)
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{
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final String referenceCodon = Character.toString(currentCodon_5to3[0]) + Character.toString(currentCodon_5to3[1]) + currentCodon_5to3[2];
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outputLineFields.put(OUTPUT_FRAME, Integer.toString(frame) );
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outputLineFields.put(OUTPUT_CODON_NUMBER, Integer.toString(codonOffset_from5) );
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outputLineFields.put(OUTPUT_PROTEIN_COORD_STR, "p."+ Integer.toString(codonOffset_from5) );
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outputLineFields.put(OUTPUT_CODING_COORD_STR, "c."+ Integer.toString(proteinOffset_from5) );
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outputLineFields.put(OUTPUT_CODON_NUMBER, Integer.toString(codonCount_from5) );
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final AminoAcid refAA = AminoAcidTable.getAA(referenceCodon, mitochondrial);
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outputLineFields.put(OUTPUT_REFERENCE_CODON, referenceCodon );
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final String refAA = AminoAcidTable.getAA3LetterCode(referenceCodon, mitochondrial);
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outputLineFields.put(OUTPUT_REFERENCE_AA, refAA);
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outputLineFields.put(OUTPUT_REFERENCE_AA, refAA.getCode());
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final char temp = currentCodon_5to3[frame];
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currentCodon_5to3[frame] = haplotypeAlternate;
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final String variantCodon = Character.toString(currentCodon_5to3[0]) + Character.toString(currentCodon_5to3[1]) + currentCodon_5to3[2];
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final String variantAA = AminoAcidTable.getAA3LetterCode(variantCodon, mitochondrial);
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final AminoAcid variantAA = AminoAcidTable.getAA(variantCodon, mitochondrial);
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outputLineFields.put(OUTPUT_VARIANT_CODON, variantCodon );
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outputLineFields.put(OUTPUT_VARIANT_AA, variantAA);
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outputLineFields.put(OUTPUT_VARIANT_AA, variantAA.getCode());
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outputLineFields.put(OUTPUT_PROTEIN_COORD_STR, "p."+ refAA.getLetter() + Integer.toString(codonCount_from5) + variantAA.getLetter() ); //for example: "p.K76A"
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currentCodon_5to3[frame] = temp;
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outputLineFields.put(OUTPUT_CHANGES_AMINO_ACID, Boolean.toString(!refAA.equals(variantAA)));
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outputLineFields.put(OUTPUT_CHANGES_AMINO_ACID, Boolean.toString(!refAA.getLetter().equals(variantAA.getLetter())));
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}
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}
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final StringBuilder codingCoordStr = new StringBuilder();
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codingCoordStr.append( mitochondrial ? "m." : "c." );
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if(positionType == PositionType.utr3) {
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codingCoordStr.append( '*' );
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}
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if(isWithinExon) {
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codingCoordStr.append( Integer.toString(codingCoord_from5) );
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} else {
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//intronic coordinates
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if(distanceToNearestSpliceSite < 0) {
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codingCoordStr.append( Integer.toString(codingCoord_from5 + 1) );
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} else {
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codingCoordStr.append( Integer.toString(codingCoord_from5 ) );
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||||
}
|
||||
codingCoordStr.append( Integer.toString( distanceToNearestSpliceSite ) );
|
||||
}
|
||||
codingCoordStr.append( haplotypeReference + ">" + haplotypeAlternate);
|
||||
outputLineFields.put(OUTPUT_CODING_COORD_STR, codingCoordStr.toString() );
|
||||
|
||||
}
|
||||
|
||||
|
||||
//write out the record
|
||||
StringBuilder outputLine = new StringBuilder();
|
||||
for( String column : OUTPUT_COLUMN_NAMES) {
|
||||
final StringBuilder outputLine = new StringBuilder();
|
||||
for( final String column : OUTPUT_COLUMN_NAMES ) {
|
||||
if(outputLine.length() != 0) {
|
||||
outputLine.append(AnnotatorROD.DELIMITER);
|
||||
outputLine.append( AnnotatorROD.DELIMITER );
|
||||
}
|
||||
String value = outputLineFields.get(column);
|
||||
final String value = outputLineFields.get(column);
|
||||
outputLine.append(value != null ? value : "");
|
||||
}
|
||||
|
||||
outputStream.println(outputLine);
|
||||
|
||||
if( !isProteinCodingTranscript ) {
|
||||
//need only one record for this position, instead of 4 (one for each allele)
|
||||
//need only one record for this position with "*" for haplotypeAlternate, instead of the 4 individual alleles
|
||||
break;
|
||||
}
|
||||
|
||||
|
|
@ -603,11 +739,12 @@ public class TranscriptToInfo extends RodWalker<Integer, Integer>
|
|||
txOffset_from5++;
|
||||
|
||||
if(positionType == PositionType.CDS) {
|
||||
proteinOffset_from5++;
|
||||
frame = (frame + 1) % 3;
|
||||
}
|
||||
|
||||
|
||||
if(isWithinExon) {
|
||||
codingCoord_from5++;
|
||||
}
|
||||
|
||||
} // l for-loop
|
||||
|
||||
|
|
|
|||
Loading…
Reference in New Issue