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formerly private class, factored out and made public. Represents a transcript annotation (transcript id, genomic location, genomic intervals for all exons present in this transcript, etc) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@834 348d0f76-0448-11de-a6fe-93d51630548a
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asivache 2009-05-27 17:52:38 +00:00
parent 8edba13ded
commit 41c1a62ac4
1 changed files with 98 additions and 0 deletions
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java/src/org/broadinstitute/sting/gatk/refdata/Transcript.java 100644
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package org.broadinstitute.sting.gatk.refdata;
import java.util.ArrayList;
import java.util.List;
import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException;
/** Holds a single transcript annotation: refseq id, gene name, genomic locations of the locus, of the coding region
* and of all the exons.
*/
class Transcript {
private String transcript_id;
private int strand;
private GenomeLoc transcript_interval;
private GenomeLoc transcript_coding_interval;
private List<GenomeLoc> exons;
private String gene_name;
private List<Integer> exon_frames;
public Transcript() {}
public Transcript(String line) {
parseLine(line);
}
/** Returns id of the transcript (RefSeq NM_* id) */
public String getTranscriptId() { return transcript_id; }
/** Returns coding strand of the transcript, 1 or -1 for positive or negative strand, respectively */
public int getStrand() { return strand; }
/** Returns transcript's full genomic interval (includes all exons with UTRs) */
public GenomeLoc getLocation() { return transcript_interval; }
/** Returns genomic interval of the coding sequence (does not include UTRs, but still includes introns, since it's a single interval on the DNA) */
public GenomeLoc getCodingLocation() { return transcript_coding_interval; }
/** Name of the gene this transcript corresponds to (NOT gene id such as Entrez etc) */
public String getGeneName() { return gene_name; }
/** Number of exons in this transcript */
public int getNumExons() { return exons.size(); }
/** Genomic location of the n-th exon; throws an exception if n is out of bounds */
public GenomeLoc getExonLocation(int n) {
if ( n >= exons.size() || n < 0 ) throw new StingException("Index out-of-bounds. Transcript has " + exons.size() +" exons; requested: "+n);
return exons.get(n);
}
/** Returns the list of all exons in this transcript, as genomic intervals */
public List<GenomeLoc> getExons() { return exons; }
/** Returns true if the specified interval 'that' overlaps with the full genomic interval of this transcript */
public boolean overlapsP (GenomeLoc that) {
return transcript_interval.overlapsP(that);
}
/** Returns true if the specified interval 'that' overlaps with the coding genomic interval of this transcript.
* NOTE: since "coding interval" is still a single genomic interval, it will not contain UTRs of the outermost exons,
* but it will still contain introns and/or exons internal to this genomic locus that are not spliced into this transcript.
* @see overlapsExonP()
*/
public boolean overlapsCodingP (GenomeLoc that) {
return transcript_coding_interval.overlapsP(that);
}
/** Returns true if the specified interval 'that' overlaps with any of the exons actually spliced into this transcript */
public boolean overlapsExonP (GenomeLoc that) {
for ( GenomeLoc e : exons ) {
if ( e.overlapsP(that) ) return true;
}
return false;
}
/** Fills this object from a text line in RefSeq (UCSC) text dump file */
public void parseLine(String line) {
String[] fields = line.split("\t");
transcript_id = fields[1];
if ( fields[3].length()==1 && fields[3].charAt(0)=='+') strand = 1;
else if ( fields[3].length()==1 && fields[3].charAt(0)=='-') strand = -1;
else throw new StingException("Expected strand symbol (+/-), found: "+fields[3]);
String contig_name = fields[2];
transcript_interval = new GenomeLoc(contig_name, Integer.parseInt(fields[4])+1, Integer.parseInt(fields[5]));
transcript_coding_interval = new GenomeLoc(contig_name, Integer.parseInt(fields[6])+1, Integer.parseInt(fields[7]));
gene_name = fields[12];
String[] exon_starts = fields[9].split(",");
String[] exon_stops = fields[10].split(",");
String[] eframes = fields[15].split(",");
assert exon_starts.length == exon_stops.length : "Data format error: numbers of exon start and stop positions differ";
assert exon_starts.length == eframes.length : "Data format error: numbers of exons and exon frameshifts differ";
exons = new ArrayList<GenomeLoc>(exon_starts.length);
exon_frames = new ArrayList<Integer>(eframes.length);
for ( int i = 0 ; i < exon_starts.length ; i++ ) {
exons.add(new GenomeLoc(contig_name, Integer.parseInt(exon_starts[i])+1, Integer.parseInt(exon_stops[i]) ) );
exon_frames.add(Integer.decode(eframes[i]));
}
}
}