/*
* 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
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* OUT OF OR IN CONNECTION WITH THE SOFTWARE OR THE USE OR OTHER DEALINGS IN
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package org.broad.igv.feature.dranger;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.exceptions.ParserException;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.feature.Strand;
import org.broad.igv.track.FeatureCollectionSource;
import org.broad.igv.track.FeatureTrack;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
import htsjdk.tribble.readers.AsciiLineReader;
import java.util.ArrayList;
import java.util.HashMap;
import java.util.List;
import java.util.Map;
/**
* @author jrobinso
*/
public class DRangerParser {
int numColumn;
int chr1Column;
int str1Column;
int pos1Column;
int chr2Column;
int str2Column;
int pos2Column;
int tumreadsColumn;
int normreadsColumn;
int classColumn;
int spanColumn;
int site1Column;
int site2Column;
int qualityColumn;
int scoreColumn;
static Logger log = Logger.getLogger(DRangerParser.class);
//num chr1 str1 pos1 chr2 str2 pos2
//1 chr1 (+) 21083863 chr1 (+) 25279578
// tumreads normreads class span site1 site2 quality score
// 48 0 long_range 4195715 3'-UTR of ENST0000037493
public List<FeatureTrack> loadTracks(ResourceLocator locator, Genome genome) {
List<FeatureTrack> tracks = new ArrayList();
AsciiLineReader reader = null;
List<htsjdk.tribble.Feature> features = new ArrayList(5000);
int parseColumn = -1;
String nextLine = null;
int rowCounter = 0;
try {
reader = ParsingUtils.openAsciiReader(locator);
setColumns(reader.readLine());
rowCounter++;
while ((nextLine = reader.readLine()) != null) {
String[] tokens = Globals.tabPattern.split(nextLine, -1);
rowCounter++;
int nTokens = tokens.length;
if (nTokens > pos2Column) {
int index = Integer.parseInt(tokens[numColumn]);
String chr1 = genome.getCanonicalChrName(tokens[chr1Column]);
int pos1 = Integer.parseInt(tokens[pos1Column]);
String str1 = tokens[str1Column];
Strand strand1 = (str1.equals("0") || str1.equals("(+)")) ? Strand.POSITIVE : Strand.NEGATIVE;
String chr2 = genome.getCanonicalChrName(tokens[chr2Column]);
int pos2 = Integer.parseInt(tokens[pos2Column]);
String str2 = tokens[str2Column];
Strand strand2 = (str2.equals("0") || str2.equals("(+)")) ? Strand.POSITIVE : Strand.NEGATIVE;
DRangerFeature feature = new DRangerFeature(chr1, pos1, strand1, chr2, pos2, strand2);
feature.setIndex(index);
if (tumreadsColumn > 0) {
feature.setTumreads(toInt(tokens[tumreadsColumn]));
}
if (normreadsColumn > 0) {
feature.setNormreads(toInt(tokens[normreadsColumn]));
}
if (classColumn > 0) {
feature.setFeatureClass(tokens[classColumn]);
}
if (spanColumn > 0) {
feature.setSpan(toInt(tokens[spanColumn]));
}
if (site1Column > 0) {
feature.setSite1(tokens[site1Column]);
}
if (site2Column > 0) {
feature.setSite2(tokens[site2Column]);
}
if (qualityColumn > 0) {
feature.setQuality(toInt(tokens[qualityColumn]));
}
if (scoreColumn > 0) {
feature.setScore(toInt(tokens[scoreColumn]));
}
features.add(feature);
}
}
} catch (NumberFormatException ne) {
throw new ParserException("Column " + parseColumn + " must be a numeric value", rowCounter, nextLine);
} catch (Exception e) {
log.error("Error parsing dRanger file", e);
if (nextLine != null && rowCounter != 0) {
throw new ParserException(e.getMessage(), e, rowCounter, nextLine);
} else {
throw new RuntimeException(e);
}
} finally {
if (reader != null) {
reader.close();
}
}
FeatureTrack track = new FeatureTrack(locator, new FeatureCollectionSource(features, genome));
track.setName(locator.getTrackName());
track.setRendererClass(DRangerRenderer.class);
tracks.add(track);
return tracks;
}
private int toInt(String token) {
try {
return Integer.parseInt(token);
} catch (NumberFormatException e) {
return 0;
}
}
private void setColumns(String header) throws Exception {
String[] tokens = header.split("\t");
Map<String, Integer> map = new HashMap();
for (int i = 0; i < tokens.length; i++) {
map.put(tokens[i].toLowerCase(), i);
}
chr1Column = map.get("chr1").intValue();
str1Column = map.get("str1").intValue();
pos1Column = map.get("pos1").intValue();
chr2Column = map.get("chr2").intValue();
str2Column = map.get("str2").intValue();
pos2Column = map.get("pos2").intValue();
if (map.containsKey("num")) {
numColumn = map.get("num").intValue();
}
if (map.containsKey("tumreads")) {
tumreadsColumn = map.get("tumreads").intValue();
}
if (map.containsKey("normreads")) {
tumreadsColumn = map.get("normreads").intValue();
}
if (map.containsKey("class")) {
classColumn = map.get("class").intValue();
}
if (map.containsKey("span")) {
spanColumn = map.get("span").intValue();
}
if (map.containsKey("site1")) {
site1Column = map.get("site1").intValue();
}
if (map.containsKey("site2")) {
site2Column = map.get("site2").intValue();
}
if (map.containsKey("quality")) {
qualityColumn = map.get("quality").intValue();
}
if (map.containsKey("score")) {
scoreColumn = map.get("score").intValue();
}
}
}