/*
* 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.broad.igv.feature.Range;
import htsjdk.tribble.AbstractFeatureReader;
import htsjdk.tribble.AsciiFeatureCodec;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Iterator;
import java.util.List;
/**
* Parses various cufflinks (and cuffdiff) output files as described here:
* <p/>
* http://cufflinks.cbcb.umd.edu/manual.html
*
* @author jrobinso
* Date: 3/8/13
* Time: 2:30 PM
*/
public class CufflinksParser {
public static List<? extends Range> parse(String path) throws IOException {
final String s = path.toLowerCase();
if (s.endsWith("fpkm_tracking")) {
AsciiFeatureCodec<FPKMValue> codec = new FPKMTrackingCodec(path);
return parse(codec, path);
} else if (s.endsWith("gene_exp.diff") || s.endsWith("cds_exp.diff")) {
AsciiFeatureCodec<ExpDiffValue> codec = new ExpDiffCodec(path);
return parse(codec, path);
} else {
throw new RuntimeException("Unsupported file type: " + path);
}
}
public static <T extends Range> List<T> parse(AsciiFeatureCodec<T> codec, String path) throws IOException {
List<T> values = new ArrayList<T>();
AbstractFeatureReader reader = AbstractFeatureReader.getFeatureReader(path, codec, false);
Iterator<T> iter = reader.iterator();
while(iter.hasNext()){
values.add(iter.next());
}
return values;
}
}