/*
* Copyright (c) 2007-2013 The Broad Institute, Inc.
* SOFTWARE COPYRIGHT NOTICE
* This software and its documentation are the copyright of the Broad Institute, Inc. All rights are reserved.
*
* This software is supplied without any warranty or guaranteed support whatsoever. The Broad Institute is not responsible for its use, misuse, or functionality.
*
* This software is licensed under the terms of the GNU Lesser General Public License (LGPL),
* Version 2.1 which is available at http://www.opensource.org/licenses/lgpl-2.1.php.
*/
package org.broad.igv.tools.converters;
import org.broad.igv.tools.parsers.DataConsumer;
import org.broad.igv.tools.parsers.ToolsWiggleParser;
import org.broad.igv.track.TrackType;
import java.io.BufferedWriter;
import java.io.FileWriter;
import java.io.IOException;
import java.io.PrintWriter;
/**
* Converts a "wig" file to a "bed" file by applying a threshold
*
* @author jrobinso
* @date Jan 20, 2011
*/
public class WigToBed implements DataConsumer {
PrintWriter bedWriter;
double lowerThreshold = 0.1;
double higherThreshold = 0.3;
String chr = null;
int featureStart = -1;
int featureEnd = -1;
String type;
private float score;
static String upperName = "upper";
static String lowerName = "lower";
public static void main(String[] args) throws IOException {
String input = args[0]; //"/Users/jrobinso/Sigma/566.wgs.bam.large_isize.wig";
WigToBed wigToBed = new WigToBed(input, .17f, .55f);
ToolsWiggleParser parser = new ToolsWiggleParser(input, wigToBed, null);
parser.parse();
}
public static void run(String inputFile, float hetThreshold, float homThreshold) throws IOException {
lowerName = String.valueOf((int) (hetThreshold * 10));
upperName = String.valueOf((int) (homThreshold * 10));
int len = inputFile.length();
String outputFile = inputFile.substring(0, len - 4) + ".bed";
WigToBed wigToBed = new WigToBed(outputFile, hetThreshold, homThreshold);
ToolsWiggleParser parser = new ToolsWiggleParser(inputFile, wigToBed, null);
parser.parse();
}
public WigToBed(String bedFile, float lowerThreshold, float higherThreshold) {
this.lowerThreshold = lowerThreshold;
this.higherThreshold = higherThreshold;
try {
bedWriter = new PrintWriter(new BufferedWriter(new FileWriter(bedFile)));
} catch (IOException e) {
e.printStackTrace(); //To change body of catch statement use File | Settings | File Templates.
}
}
public void addData(String chr, int start, int end, float[] data, String name) {
if (featureStart >= 0) {
// Feature in progress
if (start > featureEnd || data[0] < lowerThreshold) {
writeCurrentFeature();
featureStart = -1;
score = 0f;
}
featureEnd = end;
}
if (featureStart >= 0) {
if (data[0] > higherThreshold) {
type = String.valueOf(higherThreshold);
score = Math.max(score, data[0]);
} else if (data[0] < lowerThreshold) {
writeCurrentFeature();
featureStart = -1;
score = 0f;
}
} else {
if (data[0] > lowerThreshold) {
featureStart = start;
featureEnd = end;
this.chr = chr;
score = Math.max(score, data[0]);
type = data[0] > higherThreshold ? String.valueOf(higherThreshold) : String.valueOf(lowerThreshold);
}
}
}
private void writeCurrentFeature() {
bedWriter.println(this.chr + "\t" + featureStart + "\t" + featureEnd + "\t" + type);
featureStart = -1;
}
public void parsingComplete() {
if (featureStart >= 0) writeCurrentFeature();
bedWriter.close();
}
public void setTrackParameters(TrackType trackType, String trackLine, String[] trackNames) {
//To change body of implemented methods use File | Settings | File Templates.
}
public void setTrackParameters(TrackType trackType, String trackLine, String[] trackNames, boolean b) {
//To change body of implemented methods use File | Settings | File Templates.
}
/**
* Set a tolerance for "sortedness" of the data. A start position can be less than
* the immediately previous start position by this amount. This is needed for
* chip-seq processing where the start position of an alignment can be artificially
* extended post sorting.
*/
public void setSortTolerance(int tolerance) {
//To change body of implemented methods use File | Settings | File Templates.
}
public void setAttribute(String key, String value) {
//To change body of implemented methods use File | Settings | File Templates.
}
public void setType(String type) {
//To change body of implemented methods use File | Settings | File Templates.
}
}