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* The MIT License (MIT)
*
* Copyright (c) 2007-2015 Broad Institute
*
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* of this software and associated documentation files (the "Software"), to deal
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*
* The above copyright notice and this permission notice shall be included in
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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.tools.converters;
import htsjdk.samtools.util.CloseableIterator;
import htsjdk.samtools.util.SortingCollection;
import org.apache.log4j.Logger;
import org.broad.igv.data.expression.GeneToLocusHelper;
import org.broad.igv.feature.Locus;
import org.broad.igv.feature.genome.Genome;
import org.broad.igv.tools.sort.SortableRecord;
import org.broad.igv.tools.sort.SortableRecordCodec;
import org.broad.igv.track.TrackType;
import java.io.*;
import java.util.Comparator;
import java.util.List;
/**
* @author jrobinso
* @date Oct 9, 2010
* @deprecated Doesn't appear to be used anywhere, as of 23 May 2013
*/
@Deprecated
public class MageTabToIGVConverter {
private static Logger log = Logger.getLogger(MageTabToIGVConverter.class);
/**
* Parse the file and output in ".igv" format
*
* @return
*/
public static void convert(File inputFile, File outputFile, String probeResource,
int maxRecords, File tmpDir, Genome genome) throws IOException {
GeneToLocusHelper locusHelper = new GeneToLocusHelper(probeResource);
BufferedReader reader = null;
PrintWriter writer = null;
SortingCollection cltn = getSortingCollection(maxRecords, tmpDir);
try {
reader = new BufferedReader(new FileReader(inputFile));
writer = new PrintWriter(new BufferedWriter(new FileWriter(outputFile)));
// Parse the header line
String headerLine = reader.readLine();
String[] tokens = headerLine.split("\t");
//The sample names in a GCT file start at column 2,
int sampleStart = 2;
String nextLine = null;
TrackType dataType = TrackType.GENE_EXPRESSION;
while ((nextLine = reader.readLine()) != null) {
// A gct row can map to multiple loci, normally this indicates a problem with the probe
DataRow row = new DataRow(nextLine);
String probe = row.getProbe();
if (probe.startsWith("cg")) {
dataType = TrackType.DNA_METHYLATION;
}
List<Locus> loci = locusHelper.getLoci(probe, row.getDescription(), genome.getId());
if (loci == null || loci.isEmpty()) {
System.out.println("No locus found for: " + probe + " " + row.getDescription());
} else {
for (Locus locus : loci) {
String igvLine = locus.getChr() + "\t" + locus.getStart() + "\t" + locus.getEnd() + "\t" + probe +
row.getData();
cltn.add(new SortableRecord(locus.getChr(), locus.getStart(), igvLine));
}
}
}
writer.println("#type=" + dataType.toString());
writer.print("Chr\tStart\tEnd\tProbe");
for (int i = sampleStart; i < tokens.length; i++) {
writer.print("\t" + tokens[i]);
}
writer.println();
// Ouputput the sorted file
CloseableIterator<SortableRecord> iter = cltn.iterator();
while (iter.hasNext()) {
SortableRecord al = iter.next();
writer.println(al.getText());
}
} finally {
if (reader != null) {
reader.close();
}
if (writer != null) {
writer.close();
}
}
}
static SortingCollection getSortingCollection(int maxRecords, File tmpDir) {
SortableRecordCodec codec = new SortableRecordCodec();
Comparator<SortableRecord> comp = new Comparator<SortableRecord>() {
public int compare(SortableRecord o1, SortableRecord o2) {
String chr1 = o1.getChromosome().replaceFirst("chr", "");
String chr2 = o2.getChromosome().replaceFirst("chr", "");
int s1 = Integer.MAX_VALUE;
try {
s1 = Integer.parseInt(chr1);
} catch (Exception e) {
// ignore
}
int s2 = Integer.MAX_VALUE;
try {
s2 = Integer.parseInt(chr2);
} catch (Exception e) {
// ignre
}
int t1 = s1 - s2;
if (t1 == 0) {
chr1 = chr1.replace("M", "Z");
chr2 = chr2.replace("M", "Z");
t1 = chr1.compareTo(chr2);
}
if (t1 == 0) {
return (int) (o1.getStart() - o2.getStart());
} else {
return t1;
}
}
};
return SortingCollection.newInstance(SortableRecord.class, codec, comp, maxRecords, tmpDir);
}
/**
* Represents a row of data from a GCT or mage-tab file. Using this class if more effecient than tokeninzing
* the entire line. Some GCT files have over a thousand columns and we're only interested in the first 2
*/
static class DataRow {
private String probe;
private String description;
private String data;
DataRow(String string) {
int firstTab = string.indexOf('\t');
int secondTab = string.indexOf('\t', firstTab + 1);
// TODO -- if either of the indeces firstTab or secondTab are < 0 throw an exception
probe = string.substring(0, firstTab);
description = string.substring(firstTab, secondTab);
data = string.substring(secondTab);
}
private String getProbe() {
return probe;
}
public String getDescription() {
return description;
}
public String getData() {
return data;
}
}
}