/*
* 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 .exp_diff files
* @author jacob
* @date 2013-Apr-18
*/
public class ExpDiffCodec extends CufflinksCodec<ExpDiffValue>{
private static Logger log = Logger.getLogger(ExpDiffCodec.class);
int geneColumn = 1;
int locusColumn = 2;
int xColumn = 6;
int yColumn = 7;
int logRatioColumn = 8;
int sigColumn = 12;
public ExpDiffCodec(String path) {
super(ExpDiffValue.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")) geneColumn = i;
else if (tk.equals("value_1")) xColumn = i;
else if (tk.equals("value_2")) yColumn = i;
else if (tk.startsWith("log2(")) logRatioColumn = i;
else if (tk.equals("significant")) sigColumn = i;
}
return tokens;
}
//@Override
public ExpDiffValue decode(String[] tokens) {
//Skip header line
if (tokens[0].equalsIgnoreCase("test_id") || tokens[geneColumn].equalsIgnoreCase("gene_id")) {
return null;
}
if (tokens.length >= sigColumn) {
String locusString = tokens[locusColumn];
if (locusString == null) return null;
Locus locus = Locus.fromString(locusString);
if (locus == null || locus.getChr() == null) return null;
String logRatioStr = tokens[logRatioColumn];
float logRatio = Float.parseFloat(logRatioStr);
if (Float.isInfinite(logRatio) || Float.isNaN(logRatio)) {
log.info("LogRatio " + logRatioStr + " cannot be parsed as a float");
logRatio = Float.NaN;
}
float fpkmX = Float.parseFloat(tokens[xColumn]);
float fpkmY = Float.parseFloat(tokens[yColumn]);
String gene = tokens[geneColumn];
String significant = tokens[sigColumn];
return new ExpDiffValue(locus.getChr(), locus.getStart() - 1, locus.getEnd(), gene,
logRatio, fpkmX, fpkmY, significant);
} else {
log.info("Unexpected # of columns. Expected at least 12, found " + tokens.length);
return null;
}
}
@Override
public ExpDiffValue decode(String line) {
return decode(ParsingUtils.TAB_PATTERN.split(line));
}
}