/*
* Copyright (c) 2007-2012 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not
* responsible for its use, misuse, or functionality.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL), Version 2.1 which is
* available at http://www.opensource.org/licenses/lgpl-2.1.php.
*/
package org.broad.igv.methyl;
import org.broad.igv.Globals;
import org.broad.igv.bbfile.BBFileReader;
import org.broad.igv.bbfile.BedFeature;
import org.broad.igv.bbfile.BigBedIterator;
import org.broad.igv.feature.Strand;
import org.broad.igv.feature.genome.Genome;
import java.io.IOException;
import java.util.*;
import java.util.regex.Pattern;
/**
* Data source backe by Michael Ziller's custom BB format
*
* @author Jim Robinson
* @date 4/19/12
*/
public class BBMethylDataSource implements MethylDataSource {
static Pattern percentPattern = Pattern.compile("%");
enum Type {ZILLER, USC}
;
BBFileReader reader;
Type type;
/**
* Map of chr name in genome definition -> chr name in BB file. Used for reverse-lookup during queries.
*/
Map<String, String> chrNameMap;
public BBMethylDataSource(BBFileReader reader, Type type, Genome genome) throws IOException {
this.reader = reader;
this.type = type;
init(genome);
}
public Iterator<MethylScore> query(String chr, int start, int end) {
String tmp = chrNameMap.get(chr);
String querySeq = tmp == null ? chr : tmp;
BigBedIterator bedIterator = reader.getBigBedIterator(querySeq, start, chr, end, false);
return new WrappedIterator(bedIterator, type);
}
private void init(Genome genome) {
chrNameMap = new HashMap<String, String>();
if (genome != null) {
Collection<String> seqNames = reader.getChromosomeNames();
if (seqNames != null)
for (String seqName : seqNames) {
String igvChr = genome.getChromosomeAlias(seqName);
if (igvChr != null && !igvChr.equals(seqName)) {
chrNameMap.put(igvChr, seqName);
}
}
}
}
public static class WrappedIterator implements Iterator<MethylScore> {
BigBedIterator bedIterator;
Type type;
public WrappedIterator(BigBedIterator bedIterator, Type type) {
this.bedIterator = bedIterator;
this.type = type;
}
public boolean hasNext() {
return bedIterator.hasNext(); //To change body of implemented methods use File | Settings | File Templates.
}
public MethylScore next() {
BedFeature feat = null;
while (feat == null && bedIterator.hasNext()) {
feat = bedIterator.next();
String[] restOfFields = feat.getRestOfFields();
MethylScore score = type == Type.ZILLER ?
createZillerScore(feat, restOfFields) : createUSCScore(feat, restOfFields);
return score;
}
return null;
}
private MethylScore createZillerScore(BedFeature feat, String[] restOfFields) {
float percent;
float count;
String name = restOfFields[0];
if (name.contains("%")) {
//'92%[51]'
String[] tokens = percentPattern.split(name.replace("'", "").replace("[", "").replace("]", ""));
percent = Float.parseFloat(tokens[0]);
count = Float.parseFloat(tokens[1]);
} else {
// methylatedReads/totalreads
String[] tokens = Globals.forwardSlashPattern.split(name.replace("'", ""));
float methylatedReads = Float.parseFloat(tokens[0]);
count = Float.parseFloat(tokens[1]);
percent = (methylatedReads / count) * 100;
}
return new MethylScore(feat.getChromosome(), feat.getStartBase(), feat.getEndBase(), Strand.NONE, percent, (int) count);
}
private MethylScore createUSCScore(BedFeature feat, String[] restOfFields) {
//String name = restOfFields[0];
//int score = Integer.parseInt(restOfFields[1]);
char strandChar = restOfFields[2].charAt(0);
Strand strand = strandChar == '+' ? Strand.POSITIVE : (strandChar == '-' ? Strand.NEGATIVE : Strand.NONE);
float percentMethyl = Float.parseFloat(restOfFields[3]);
int count = Integer.parseInt(restOfFields[4]);
return new MethylScore(feat.getChromosome(), feat.getStartBase(), feat.getEndBase(), strand, percentMethyl, count);
}
public void remove() {
//To change body of implemented methods use File | Settings | File Templates.
}
}
}