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changed to use factored out Transcript class; some docs added (not much) 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@836 348d0f76-0448-11de-a6fe-93d51630548a
This commit is contained in:
asivache 2009-05-27 18:17:23 +00:00
parent ae0bac5696
commit 5b310e48f5
1 changed files with 59 additions and 103 deletions
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162
java/src/org/broadinstitute/sting/playground/gatk/refdata/rodRefSeq.java
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@ -2,15 +2,14 @@ package org.broadinstitute.sting.playground.gatk.refdata;
import java.io.File; import java.io.File;
import java.io.IOException; import java.io.IOException;
import java.util.ArrayList;
import java.util.Collections; import java.util.Collections;
import java.util.Iterator; import java.util.Iterator;
import java.util.LinkedList; import java.util.LinkedList;
import java.util.List; import java.util.List;
import java.util.zip.DataFormatException;
import org.broadinstitute.sting.gatk.iterators.PushbackIterator; import org.broadinstitute.sting.gatk.iterators.PushbackIterator;
import org.broadinstitute.sting.gatk.refdata.BasicReferenceOrderedDatum; import org.broadinstitute.sting.gatk.refdata.BasicReferenceOrderedDatum;
import org.broadinstitute.sting.gatk.refdata.Transcript;
import org.broadinstitute.sting.utils.GenomeLoc; import org.broadinstitute.sting.utils.GenomeLoc;
import org.broadinstitute.sting.utils.StingException; import org.broadinstitute.sting.utils.StingException;
import org.broadinstitute.sting.utils.xReadLines; import org.broadinstitute.sting.utils.xReadLines;
@ -18,14 +17,20 @@ import org.broadinstitute.sting.utils.xReadLines;
public class rodRefSeq extends BasicReferenceOrderedDatum { public class rodRefSeq extends BasicReferenceOrderedDatum {
private GenomeLoc location = null; private GenomeLoc location = null;
private List<RefSeqRecord> records = null; private List<Transcript> records = null;
public rodRefSeq(String name) { public rodRefSeq(String name) {
super(name); super(name);
// location = new GenomeLoc(0,0,-1); // location = new GenomeLoc(0,0,-1);
} }
public rodRefSeq(String name, GenomeLoc location, List<RefSeqRecord> records) { /** Despite this constructor is public, it is meant primarily for the internal use; RefSeq iterator will
* call it to populate the ROD at the given genomic location with the data (transcripts) it is holding
* @param name
* @param location
* @param records
*/
public rodRefSeq(String name, GenomeLoc location, List<Transcript> records) {
super(name); super(name);
this.location = location; this.location = location;
this.records = records; this.records = records;
@ -36,28 +41,37 @@ public class rodRefSeq extends BasicReferenceOrderedDatum {
return location; return location;
} }
/** Required by ReferenceOrderedDatum interface; this method does nothing (always returns false),
* since this rod provides its own iterator for reading underlying data files.
*/
@Override @Override
public boolean parseLine(Object header, String[] parts) { public boolean parseLine(Object header, String[] parts) {
return false; // this rod has its own iterator return false; // this rod has its own iterator
} }
/** Returns true if the current position this ROD is associated with is within the coding interval for at least
* one of the annotated transcripts. NOTE: "coding" interval is defined as a single genomic interval, so it
* does not include the UTRs of the outermost exons, but it includes introns between exons spliced into a
* transcript, or internal exons that are not spliced into a given transcript. @see isExon().
* @return
*/
public boolean isCoding() { public boolean isCoding() {
if ( records == null ) return false; if ( records == null ) return false;
for ( RefSeqRecord r : records) { for ( Transcript t : records) {
if (location.getStart() >= r.getCodingLocation().getStart() && location.getStart() <= r.getCodingLocation().getStop() ) return true; if ( t.overlapsCodingP(location) ) return true;
} }
return false; return false;
} }
/** Returns true if the current position this ROD is associated with is within an exon for at least
* one of the annotated transcripts. NOTE: position can be still within a UTR, see @isCoding()
* @return
*/
public boolean isExon() { public boolean isExon() {
if ( records == null ) return false; if ( records == null ) return false;
for ( RefSeqRecord r : records) { for ( Transcript t : records) {
for ( GenomeLoc e : r.getExons() ) { if ( t.overlapsExonP(location) ) return true;
// System.err.println("EXON: "+e);
if (location.getStart() >= e.getStart() && location.getStart() <= e.getStop() ) return true;
}
} }
return false; return false;
} }
@ -67,17 +81,18 @@ public class rodRefSeq extends BasicReferenceOrderedDatum {
throw new StingException("repl() is not implemented yet"); throw new StingException("repl() is not implemented yet");
} }
/** Will print the genomic location of this rod, followed by (space separated) ids of all the
* annotated transcripts overlapping with this position.
*/
@Override @Override
public String toSimpleString() { public String toSimpleString() {
if ( records == null ) return new String(getName()+": <NULL>"); if ( records == null ) return new String(getName()+": <NULL>");
StringBuilder b = new StringBuilder(); StringBuilder b = new StringBuilder();
b.append(getName()); b.append(getName());
b.append(":"); b.append(":");
for ( RefSeqRecord r : records ) { for ( Transcript t : records ) {
b.append(' '); b.append(' ');
b.append(r.getTranscriptId()); b.append(t.getTranscriptId());
// b.append("; "+ r.getNumExons() + " exons: ");
// for ( GenomeLoc e : r.getExons() ) b.append(" " + e);
} }
return b.toString(); return b.toString();
} }
@ -87,8 +102,8 @@ public class rodRefSeq extends BasicReferenceOrderedDatum {
return toSimpleString(); return toSimpleString();
} }
public static Iterator<rodRefSeq> createIterator(String trackName, File f) throws IOException, DataFormatException { public static Iterator<rodRefSeq> createIterator(String trackName, File f) throws IOException {
return new refSeqIterator(f, trackName); return new refSeqIterator(trackName,f);
} }
} }
@ -98,13 +113,13 @@ class refSeqIterator implements Iterator<rodRefSeq> {
private long curr_position = 0; private long curr_position = 0;
private long max_position = 0; private long max_position = 0;
private String curr_contig_name = null; // will keep the name of the contig the iterator is currently in private String curr_contig_name = null; // will keep the name of the contig the iterator is currently in
private List<RefSeqRecord> records; // will keep the list of all transcripts overlapping with the current position private List<Transcript> records; // will keep the list of all transcripts overlapping with the current position
private PushbackIterator<RefSeqRecord> reader; private PushbackIterator<Transcript> reader;
private String name = null; private String name = null;
public refSeqIterator(File f, String trackName) throws IOException { public refSeqIterator(String trackName, File f) throws IOException {
reader = new PushbackIterator<RefSeqRecord>( new refSeqRecordIterator(f) ); reader = new PushbackIterator<Transcript>( new refSeqRecordIterator(f) );
records = new LinkedList<RefSeqRecord>(); records = new LinkedList<Transcript>();
name = trackName; name = trackName;
} }
@ -124,11 +139,10 @@ class refSeqIterator implements Iterator<rodRefSeq> {
if ( curr_position <= max_position ) { if ( curr_position <= max_position ) {
// we still have bases covered by at least one currently loaded transcript; // we still have bases covered by at least one currently loaded transcript;
// we have to purge only subset of transcripts, on which we moved past the end // we have to purge only subset of transcripts, on which we moved past the end
Iterator<RefSeqRecord> i = records.iterator(); Iterator<Transcript> i = records.iterator();
while ( i.hasNext() ) { while ( i.hasNext() ) {
RefSeqRecord r = i.next(); Transcript t = i.next();
if ( r.getLocation().getStop() < curr_position ) { if ( t.getLocation().getStop() < curr_position ) {
System.out.println("Throwing away: " + r.toString());
i.remove(); // we moved past the end of transcript r, purge it forever i.remove(); // we moved past the end of transcript r, purge it forever
} }
} }
@ -136,29 +150,29 @@ class refSeqIterator implements Iterator<rodRefSeq> {
// ooops, we are past the end of all loaded transcripts - kill them all, // ooops, we are past the end of all loaded transcripts - kill them all,
// load next transcript and fastforward current position to its start // load next transcript and fastforward current position to its start
records.clear(); records.clear();
RefSeqRecord r = reader.next(); // if hasNext() previously returned true, we are guaranteed that this call to reader.next() is safe Transcript t = reader.next(); // if hasNext() previously returned true, we are guaranteed that this call to reader.next() is safe
records.add( r ); records.add( t );
curr_contig_name = r.getLocation().getContig(); curr_contig_name = t.getLocation().getContig();
curr_position = r.getLocation().getStart(); curr_position = t.getLocation().getStart();
max_position = r.getLocation().getStop(); max_position = t.getLocation().getStop();
} }
// 'records' only keeps those transcripts now, on which we did not reach the end yet // 'records' only keeps those transcripts now, on which we did not reach the end yet
// (we might have reloaded records completely if it was necessary); current position is correctly set. // (we might have reloaded records completely if it was necessary); current position is correctly set.
// lets check if we walked into new transcripts so we'd need to load them too: // lets check if we walked into additional new transcripts so we'd need to load them too:
while ( reader.hasNext() ) { while ( reader.hasNext() ) {
RefSeqRecord r = reader.peek(); Transcript t = reader.peek();
int ci1 = GenomeLoc.getContigIndex(curr_contig_name); int ci1 = GenomeLoc.getContigIndex(curr_contig_name);
int ci2 = GenomeLoc.getContigIndex( r.getLocation().getContig() ); int ci2 = GenomeLoc.getContigIndex( t.getLocation().getContig() );
if ( ci1 > ci2 ) throw new StingException("RefSeq track seems to be not contig-ordered"); if ( ci1 > ci2 ) throw new StingException("RefSeq track seems to be not contig-ordered");
if ( ci1 < ci2 ) break; // next transcript is on the next contig, we do not need it yet... if ( ci1 < ci2 ) break; // next transcript is on the next contig, we do not need it yet...
if ( r.getLocation().getStart() > curr_position ) break; // next transcript is on the same contig but starts after the current position; we are done if ( t.getLocation().getStart() > curr_position ) break; // next transcript is on the same contig but starts after the current position; we are done
r = reader.next(); // we need next record, time to load it for real t = reader.next(); // we do need next record, time to load it for real
long stop = r.getLocation().getStop(); long stop = t.getLocation().getStop();
if ( stop < curr_position ) throw new StingException("DEBUG: encuntered contig that should have been loaded earlier"); if ( stop < curr_position ) throw new StingException("DEBUG: encountered contig that should have been loaded earlier");
if ( stop > max_position ) max_position = stop; if ( stop > max_position ) max_position = stop;
records.add(r); records.add(t);
} }
// 'records' and current position are fully updated. We can now create new rod and return it (NOTE: this iterator will break if the list // 'records' and current position are fully updated. We can now create new rod and return it (NOTE: this iterator will break if the list
@ -179,7 +193,7 @@ class refSeqIterator implements Iterator<rodRefSeq> {
/** Low-level iterator for reading refseq annotation file record by record (i.e. line by line). Returns /** Low-level iterator for reading refseq annotation file record by record (i.e. line by line). Returns
* pre-processed input lines as RefSeqRecord objects. * pre-processed input lines as RefSeqRecord objects.
*/ */
class refSeqRecordIterator implements Iterator<RefSeqRecord> { class refSeqRecordIterator implements Iterator<Transcript> {
private xReadLines reader; private xReadLines reader;
@ -191,10 +205,10 @@ class refSeqRecordIterator implements Iterator<RefSeqRecord> {
} }
@Override @Override
public RefSeqRecord next() { public Transcript next() {
RefSeqRecord r = new RefSeqRecord(); Transcript t = new Transcript();
r.parseLine( reader.next() ); t.parseLine( reader.next() );
return r; return t;
} }
@ -206,61 +220,3 @@ class refSeqRecordIterator implements Iterator<RefSeqRecord> {
} }
/** Holds a single transcript annotation: refseq id, gene name, genomic locations of the locus, of the coding region
* and of all the exons.
*/
class RefSeqRecord {
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 RefSeqRecord() {}
public RefSeqRecord(String line) throws DataFormatException {
parseLine(line);
}
public String getTranscriptId() { return transcript_id; }
public int getStrand() { return strand; }
public GenomeLoc getLocation() { return transcript_interval; }
public GenomeLoc getCodingLocation() { return transcript_coding_interval; }
public String getGeneName() { return gene_name; }
public int getNumExons() { return exons.size(); }
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);
}
public List<GenomeLoc> getExons() { return exons; }
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]));
}
}
}