/*
* 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.data.cufflinks;
import org.apache.log4j.Logger;
import org.broad.igv.feature.Locus;
import org.broad.igv.util.ParsingUtils;
/**
* Codec for Cufflinks FPKM files, extension fpkm_tracking
*
* @author jacob
* @date 2013-Apr-18
*/
public class FPKMTrackingCodec extends CufflinksCodec<FPKMValue>{
private static Logger log = Logger.getLogger(FPKMTrackingCodec.class);
int geneColumn = 4;
int locusColumn = 6;
static final int startfpkmCol = 9;
static final int colsPerSample = 4;
private int numSamples = 1;
public FPKMTrackingCodec(String path){
super(FPKMValue.class, path);
}
@Override
public Object readHeader(String[] tokens) {
for(int i=0; i<tokens.length; i++) {
final String tk = tokens[i];
if(tk.equals("locus")) locusColumn = i;
else if(tk.equals("gene_short_name")) geneColumn = i;
}
numSamples = (tokens.length - startfpkmCol) / colsPerSample;
return tokens;
}
@Override
public FPKMValue decode(String line) {
return decode(ParsingUtils.TAB_PATTERN.split(line));
}
//@Override
public FPKMValue decode(String[] tokens) {
//Skip header line
if (tokens[0].equalsIgnoreCase("tracking_id") || tokens[geneColumn].equalsIgnoreCase("gene_short_name")) {
return null;
}
if (tokens.length >= (startfpkmCol + numSamples*colsPerSample)) {
String locusString = tokens[locusColumn];
if (locusString == null) return null;
Locus locus = Locus.fromString(locusString);
if(locus == null || locus.getChr() == null) return null;
String gene = tokens[geneColumn];
float[] fpkm = new float[numSamples];
float[] confLo = new float[numSamples];
float[] confHi = new float[numSamples];
for(int sampNum = 0; sampNum < numSamples; sampNum++){
int startCol = startfpkmCol + sampNum*colsPerSample;
fpkm[sampNum] = Float.parseFloat(tokens[startCol]);
confLo[sampNum] = Float.parseFloat(tokens[startCol+1]);
confHi[sampNum] = Float.parseFloat(tokens[startCol+2]);
}
return new FPKMValue(locus.getChr(), locus.getStart() - 1, locus.getEnd(), gene,
fpkm, confLo, confHi);
} else {
log.info("Unexpected # of columns. Expected at least 12, found " + tokens.length);
return null;
}
}
public int getNumSamples() {
return numSamples;
}
}