/*
* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
* Permission is hereby granted, free of charge, to any person obtaining a copy
* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
* to use, copy, modify, merge, publish, distribute, sublicense, and/or sell
* copies of the Software, and to permit persons to whom the Software is
* furnished to do so, subject to the following conditions:
*
* The above copyright notice and this permission notice shall be included in
* all copies or substantial portions of the Software.
*
*
* THE SOFTWARE IS PROVIDED "AS IS", WITHOUT WARRANTY OF ANY KIND, EXPRESS OR
* IMPLIED, INCLUDING BUT NOT LIMITED TO THE WARRANTIES OF MERCHANTABILITY,
* FITNESS FOR A PARTICULAR PURPOSE AND NONINFRINGEMENT. IN NO EVENT SHALL THE
* AUTHORS OR COPYRIGHT HOLDERS BE LIABLE FOR ANY CLAIM, DAMAGES OR OTHER
* LIABILITY, WHETHER IN AN ACTION OF CONTRACT, TORT OR OTHERWISE, ARISING FROM,
* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
* THE SOFTWARE.
*/
/*
* GisticFilesParser.java
*
* Created on June 22, 2007, 8:32 AM
*
* To change this template, choose Tools | Template Manager
* and open the template in the editor.
*/
package org.broad.igv.feature;
//~--- non-JDK imports --------------------------------------------------------
import org.apache.log4j.Logger;
import org.broad.igv.exceptions.ParserException;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.genome.GenomeManager;
import org.broad.igv.track.GisticTrack;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
import htsjdk.tribble.readers.AsciiLineReader;
import java.io.FileNotFoundException;
import java.util.ArrayList;
import java.util.List;
/**
* @author jrobinso
*/
public class GisticFileParser {
private static Logger log = Logger.getLogger(GisticFileParser.class);
/**
* Method description
*
* @param locator
* @return
*/
public static GisticTrack loadData(ResourceLocator locator) {
// TODO -- handle remote resource
AsciiLineReader reader = null;
String nextLine = null;
int rowCounter = 0;
try {
Genome genome = GenomeManager.getInstance().getCurrentGenome();
reader = ParsingUtils.openAsciiReader(locator);
// Parse header
reader.readLine();
rowCounter++;
// Parse data
// parameters to track chromosome breaks. Used in wholeGenome case.
GisticTrack track = new GisticTrack(locator);
track.setName(locator.getTrackName());
List<GisticScore> scores = new ArrayList();
nextLine = reader.readLine();
rowCounter++;
while ((nextLine != null) && (nextLine.length() > 0)) {
String[] tokens = nextLine.split("\t");
GisticScore.Type type = getType(tokens[0].trim());
String chr = genome.getCanonicalChrName(tokens[1].trim());
int start = -1;
try {
start = Integer.parseInt(tokens[2]);
}
catch (NumberFormatException ne) {
throw new ParserException("Column 3 must be a numeric value.", rowCounter, nextLine);
}
int end = -1;
try {
end = Integer.parseInt(tokens[3]);
}
catch (NumberFormatException ne) {
throw new ParserException("Column 4 must be a numeric value.", rowCounter, nextLine);
}
float qValue = 0;
try {
qValue = Float.parseFloat(tokens[4]);
} catch (NumberFormatException numberFormatException) {
if (tokens[4].toLowerCase().equals("inf")) {
qValue = Float.POSITIVE_INFINITY;
} else {
qValue = Float.NaN;
}
}
try {
float gScore = Float.parseFloat(tokens[5]);
scores.add(new GisticScore(chr, start, end, qValue, gScore, type));
}
catch (Exception ex) {
log.error("Skipping line: " + nextLine, ex);
}
nextLine = reader.readLine();
rowCounter++;
}
if (scores.isEmpty()) {
throw new RuntimeException("No gistic scores were found.");
} else {
track.setScores(scores);
computeWholeGenome(track, genome);
return track;
}
} catch (FileNotFoundException e) {
log.error("File not found: " + locator.getPath());
throw new RuntimeException(e);
}
catch (ParserException e) {
throw new RuntimeException(e);
}
catch (Exception e) {
log.error("Exception when loading: " + locator.getPath(), e);
if (rowCounter != 0) {
throw new ParserException(e.getMessage(), rowCounter, nextLine);
} else {
throw new RuntimeException(e);
}
} finally {
if (reader != null) {
reader.close();
}
}
}
/**
* Compute features for "chr All". This is probably not the best way to do this,
* definitely not good for large tracks. Need it now for mutation data.
*
* @param track
*/
public static void computeWholeGenome(GisticTrack track, Genome genome) {
int unit = 1000; // KB
String chrAll = "All";
List<GisticScore> allFeatures = new ArrayList(1000);
if (genome == null) {
throw new RuntimeException("Unknown genome: " + genome.getId());
}
genome.getLongChromosomeNames();
long offset = 0;
for (String chr : genome.getLongChromosomeNames()) {
int chrLength = genome.getChromosome(chr).getLength();
int chrStart = (int) (offset / unit);
allFeatures.add(new GisticScore(chrAll, chrStart, chrStart, 0, 0, GisticScore.Type.AMP));
allFeatures.add(new GisticScore(chrAll, chrStart, chrStart, 0, 0, GisticScore.Type.DEL));
List<GisticScore> ampScores = track.getAmpScores(chr);
if (ampScores != null) {
for (GisticScore m : ampScores) {
int start = genome.getGenomeCoordinate(chr, m.getStart());
int end = genome.getGenomeCoordinate(chr, m.getEnd());
allFeatures.add(new GisticScore(chrAll, start, end,
(float) m.getQValue(),
(float) m.getGScore(),
m.getType()));
}
}
List<GisticScore> delScores = track.getDelScores(chr);
if (delScores != null) {
for (GisticScore m : delScores) {
int start = (int) ((offset + m.getStart()) / unit);
int end = (int) ((offset + m.getEnd()) / unit);
allFeatures.add(new GisticScore(chrAll, start, end,
(float) m.getQValue(),
(float) m.getGScore(),
m.getType()));
}
}
offset += chrLength;
}
track.setScores(allFeatures);
}
static GisticScore.Type getType(String typeString) {
if (typeString.toUpperCase().equals("AMP")) {
return GisticScore.Type.AMP;
} else if (typeString.toUpperCase().equals("DEL")) {
return GisticScore.Type.DEL;
} else {
throw new IllegalArgumentException("Unkown score type: " + typeString);
}
}
}