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*
* Copyright (c) 2007-2015 Broad Institute
*
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* of this software and associated documentation files (the "Software"), to deal
* in the Software without restriction, including without limitation the rights
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* 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.
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*
* 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
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package org.broad.igv.feature.tribble;
import org.apache.log4j.Logger;
import org.broad.igv.Globals;
import org.broad.igv.exceptions.DataLoadException;
import org.broad.igv.feature.Mutation;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.util.ParsingUtils;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.collections.MultiMap;
import htsjdk.tribble.AsciiFeatureCodec;
import htsjdk.tribble.readers.AsciiLineReader;
import htsjdk.tribble.readers.LineIterator;
import htsjdk.tribble.readers.LineIteratorImpl;
import java.io.BufferedReader;
import java.io.IOException;
/**
* Codec for .mut and .maf mutation files
*
* @author jrobinso
* Date: 10/24/12
* Time: 12:05 PM
*/
public class MUTCodec extends AsciiFeatureCodec<Mutation> {
private static Logger log = Logger.getLogger(MUTCodec.class);
private String path; // for error messages
private boolean isMAF;
private String[] headers;
private String[] samples;
private Genome genome;
private int chrColumn;
private int startColumn;
private int endColumn;
private int sampleColumn;
private int typeColumn;
private int refAlleleColumn;
private int tumorAllele1Column;
private int tumorAllele2Column;
private int errorCount = 0;
public MUTCodec(String path, Genome genome) {
super(Mutation.class);
this.path = path;
this.genome = genome;
try {
LineIterator reader = new LineIteratorImpl(new AsciiLineReader(ParsingUtils.openInputStream(path)));
readActualHeader(reader);
} catch (IOException e) {
log.error(e.getMessage(), e);
}
}
public Void readActualHeader(LineIterator reader) {
String nextLine = null;
while (reader.hasNext()) {
nextLine = reader.peek();
if (nextLine.startsWith("#")) {
if (nextLine.startsWith("#samples")) {
String[] tokens = Globals.whitespacePattern.split(nextLine, 2);
if (tokens.length < 2) {
log.error("Error parsing sample header in mutation file: " + path);
} else {
samples = Globals.commaPattern.split(tokens[1]);
for (int i = 0; i < samples.length; i++) {
samples[i] = samples[i].trim();
}
}
}
reader.next();
continue;
}
String[] tokens = Globals.tabPattern.split(nextLine);
if (tokens.length >= 5) {
reader.next();
headers = tokens;
isMAF = headers.length >= 16 && headers[0].equalsIgnoreCase("Hugo_Symbol");
setColumns(isMAF);
return null;
} else {
throw new RuntimeException(String.format("Not enough columns in header line found in %s: %s", path, nextLine));
}
}
throw new RuntimeException("Unexpected end-of-file (no header line): " + path);
}
public String[] getSamples() {
return samples;
}
public int getChrColumn() {
return chrColumn;
}
public int getStartColumn() {
return startColumn;
}
@Override
public Mutation decode(String line) {
if (line.startsWith("#") || line.startsWith("Hugo_Symbol")) {
return null;
} else {
String[] tokens = Globals.tabPattern.split(line);
String chr = genome == null ? tokens[chrColumn].trim() : genome.getCanonicalChrName(tokens[chrColumn].trim());
int start;
try {
start = Integer.parseInt(tokens[startColumn].trim());
} catch (NumberFormatException e) {
errorCount++;
if(errorCount > 100) {
throw new DataLoadException("Column " + (startColumn + 1) + " must be a numeric value.", path);
}
else {
log.info("Error parsing line: " + line);
return null;
}
}
int end;
try {
end = Integer.parseInt(tokens[endColumn].trim());
} catch (NumberFormatException e) {
errorCount++;
if(errorCount > 100) {
throw new DataLoadException("Column " + (endColumn + 1) + " must be a numeric value.", path);
}
else {
log.info("Error parsing line: " + line);
return null;
}
}
// MAF files use the 1-based inclusive convention for coordinates. The convention is not
// specified for MUT files, and it appears both conventions have been used. We can detect
// the convention used for single base mutations by testing start == end.
if (isMAF || (start == end)) {
start--;
}
String sampleId = tokens[sampleColumn].trim();
String type = tokens[typeColumn].trim();
MultiMap<String, String> attributes = new MultiMap();
int n = Math.min(headers.length, tokens.length);
for (int i = 0; i < n; i++) {
String key = headers[i];
String value = tokens[i];
if (value.length() > 0) {
attributes.put(key, value);
}
}
Mutation mut = new Mutation(sampleId, chr, start, end, type);
mut.setAttributes(attributes);
if (refAlleleColumn > 0) {
mut.setRefAllele(tokens[refAlleleColumn].trim());
}
if (tumorAllele1Column > 0) {
mut.setAltAllele1(tokens[tumorAllele1Column].trim());
}
if (tumorAllele2Column > 0) {
mut.setAltAllele2(tokens[tumorAllele2Column].trim());
}
return mut;
}
}
private void setColumns(boolean isMAF) {
this.isMAF = isMAF;
if (isMAF) {
chrColumn = 4;
startColumn = 5;
endColumn = 6;
sampleColumn = 15;
typeColumn = 8;
refAlleleColumn = 10;
tumorAllele1Column = 11;
tumorAllele2Column = 12;
} else {
chrColumn = 0;
startColumn = 1;
endColumn = 2;
sampleColumn = 3;
typeColumn = 4;
refAlleleColumn = -1;
tumorAllele1Column = -1;
tumorAllele2Column = -1;
}
}
/**
* @param locator
* @return
* @throws IOException
*/
public static boolean isMutationAnnotationFile(ResourceLocator locator) {
String ext;
{
//Only want pathLC when checking extension, so we limit its scope
String typeStringLC = locator.getTypeString().toLowerCase();
if (typeStringLC.endsWith(".maf.annotated")) {
// TCGA extension
return true;
}
ext = ParsingUtils.getIGVExtension(typeStringLC);
}
if (ext.equals("mut")) {
return true;
} else if (ext.equals("maf")) {
BufferedReader reader = null;
String path = locator.getPath();
try {
reader = ParsingUtils.openBufferedReader(path);
if (reader == null) {
return false;
}
String nextLine;
while ((nextLine = reader.readLine()) != null && nextLine.startsWith("#")) {
if (nextLine.startsWith("#")) {
continue;
}
}
String[] tokens = nextLine.split("\t");
return tokens.length > 15 && tokens[0].equalsIgnoreCase("Hugo_Symbol");
} catch (IOException e) {
log.error("Error reading: " + path, e);
return false;
} finally {
if (reader != null) {
try {
reader.close();
} catch (IOException e) {
log.error("Error closing: " + path, e);
}
}
}
} else {
return false;
}
}
@Override
public boolean canDecode(String path) {
String fn = path.toLowerCase();
if (fn.endsWith(".gz")) fn = fn.substring(0, fn.length() - 3);
return fn.endsWith(".narrowpeak") || fn.endsWith(".broadpeak");
}
}