/*
* 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.
*/
package org.broad.igv.data.seg;
//~--- non-JDK imports --------------------------------------------------------
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.exceptions.DataLoadException;
import org.broad.igv.exceptions.ParserException;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.track.TrackType;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
import htsjdk.tribble.readers.AsciiLineReader;
/**
* Example
* CCLE_name chrom loc.start loc.end num.mark seg.mean
* A2780_OVARY 1 51598 88465 17 1.0491
* A2780_OVARY 1 218569 55606710 30512 0.0248
* A2780_OVARY 1 55606801 61331401 4399 -0.0431
*
* @author jrobinso
*/
public class SegmentFileParser implements SegFileParser {
enum Type {
SEG, BIRDSUITE, NEXUS
}
;
private static Logger log = Logger.getLogger(SegmentFileParser.class);
boolean birdsuite = false;
int sampleColumn = 0;
int chrColumn = 1;
int startColumn = 2;
int endColumn = 3;
//int snpCountColumn = 4; // Default value
int dataColumn = 5; // Default value
ResourceLocator locator;
/**
* Constructs ...
*
* @param locator
*/
public SegmentFileParser(ResourceLocator locator) {
this.locator = locator;
if (locator.getPath().toLowerCase().endsWith("birdseye_canary_calls")) {
birdsuite = true;
}
}
/**
* Return a map of trackId -> segment datasource
*
* @return
*/
public SegmentedAsciiDataSet loadSegments(ResourceLocator locator, Genome genome) {
SegmentedAsciiDataSet dataset = new SegmentedAsciiDataSet(genome);
if (birdsuite) {
dataset.setTrackType(TrackType.CNV);
}
AsciiLineReader reader = null;
String nextLine = null;
int lineNumber = 0;
try {
reader = ParsingUtils.openAsciiReader(locator);
// Parse comments, if any
nextLine = reader.readLine();
while (nextLine.startsWith("#") || (nextLine.trim().length() == 0)) {
lineNumber++;
if (nextLine.length() > 0) {
parseComment(nextLine, dataset);
}
nextLine = reader.readLine();
}
// Read column headings
String[] headings = nextLine.split("\t");
if (birdsuite) {
//sample sample_index copy_number chr start end confidence
sampleColumn = 0;
dataColumn = 2;
chrColumn = 3;
startColumn = 4;
endColumn = 5;
} else {
sampleColumn = 0;
chrColumn = 1;
startColumn = 2;
endColumn = 3;
dataColumn = headings.length - 1;
}
while ((nextLine = reader.readLine()) != null && (nextLine.trim().length() > 0)) {
lineNumber++;
String[] tokens = Globals.tabPattern.split(nextLine, -1);
int nTokens = tokens.length;
if (nTokens > 4) {
int start;
int end;
try {
start = ParsingUtils.parseInt(tokens[startColumn].trim());
} catch (NumberFormatException numberFormatException) {
throw new ParserException("Column " + (startColumn + 1) + " must contain a numeric value.",
lineNumber, nextLine);
}
try {
end = ParsingUtils.parseInt(tokens[endColumn].trim());
} catch (NumberFormatException numberFormatException) {
throw new ParserException("Column " + (endColumn + 1) + " must contain a numeric value.",
lineNumber, nextLine);
}
String chr = tokens[chrColumn].trim();
if (genome != null) {
chr = genome.getCanonicalChrName(chr);
}
String trackId = new String(tokens[sampleColumn].trim());
StringBuffer desc = null;
if (birdsuite) {
desc = new StringBuffer();
desc.append("<br>");
desc.append(headings[6]);
desc.append("=");
desc.append(tokens[6]);
} else {
if (tokens.length > 4) {
desc = new StringBuffer();
for (int i = 4; i < headings.length - 1; i++) {
desc.append("<br>");
desc.append(headings[i]);
desc.append(": ");
desc.append(tokens[i]);
}
}
}
try {
float value = Float.parseFloat(tokens[dataColumn]);
String description = desc == null ? null : desc.toString();
dataset.addSegment(trackId, chr, start, end, value, description);
} catch (NumberFormatException numberFormatException) {
// log.info("Skipping line: " + nextLine);
}
}
}
} catch (DataLoadException pe) {
throw pe;
} catch (ParserException pe) {
throw pe;
} catch (Exception e) {
if (nextLine != null && lineNumber != 0) {
throw new ParserException(e.getMessage(), e, lineNumber, nextLine);
} else {
throw new RuntimeException(e);
}
} finally {
if (reader != null) {
reader.close();
}
}
dataset.sortLists();
return dataset;
}
/**
* Note: This is an exact copy of the method in ExpressionFileParser. Refactor to merge these
* two parsers, or share a common base class.
*
* @param comment
* @param dataset
*/
private void parseComment(String comment, SegmentedAsciiDataSet dataset) {
String tmp = comment.substring(1, comment.length());
if (tmp.startsWith("track")) {
ParsingUtils.parseTrackLine(tmp, dataset.getTrackProperties());
} else {
String[] tokens = tmp.split("=");
String key = tokens[0].trim().toLowerCase();
if (key.equals("type")) {
if (tokens.length != 2) {
return;
}
try {
dataset.setTrackType(TrackType.valueOf(tokens[1].trim().toUpperCase()));
} catch (Exception exception) {
log.error("Unknown track type: " + tokens[1].trim().toUpperCase());
}
}
}
}
}