/*
* Copyright (c) 2007-2012 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.gwas;
import org.broad.igv.AbstractHeadlessTest;
import org.broad.igv.exceptions.ParserException;
import org.broad.igv.track.Track;
import org.broad.igv.track.TrackLoader;
import org.broad.igv.util.ResourceLocator;
import org.broad.igv.util.TestUtils;
import org.broad.igv.util.collections.DoubleArrayList;
import org.broad.igv.util.collections.IntArrayList;
import org.junit.Test;
import java.util.LinkedHashMap;
import java.util.List;
import static junit.framework.Assert.*;
/**
* User: jacob
* Date: 2012/04/18
*/
public class GWASParserTest extends AbstractHeadlessTest {
@Test
public void testParse_underflows() throws Exception {
GWASParser parser = new GWASParser(new ResourceLocator(TestUtils.DATA_DIR + "gwas/smallp.gwas"), genome);
GWASData data = parser.parse();
LinkedHashMap<String, DoubleArrayList> values = data.getValues();
for (String chr : values.keySet()) {
DoubleArrayList floats = values.get(chr);
for (int ff = 0; ff < floats.size(); ff++) {
double val = floats.get(ff);
assertFalse("Value is infinite", Double.isInfinite(val));
assertFalse("Value isNan", Double.isNaN(val));
assertFalse("Value is 0", val == 0.0f);
}
}
}
@Test
public void testParseStarts() throws Exception {
GWASParser parser = new GWASParser(new ResourceLocator(TestUtils.DATA_DIR + "gwas/smallp.gwas"), genome);
GWASData data = parser.parse();
IntArrayList startLocs = data.getLocations().get("chr6");
int[] expStarts = {29622220,29623739,29623739};
for(int ii=0; ii < expStarts.length; ii++){
assertEquals(expStarts[ii], startLocs.get(ii));
}
}
@Test
public void testBadPs() throws Exception {
String[] finames = {"badp_neg.gwas", "badp_text.gwas", "badp_zero.gwas"};
for (String finame : finames) {
tstParseBad(finame);
}
}
@Test
public void testUnsorted() throws Exception{
String path = "random.gwas";
tstParseBad(path);
}
public void tstParseBad(String finame) throws Exception {
GWASParser parser = new GWASParser(new ResourceLocator(TestUtils.DATA_DIR + "gwas/" + finame), genome);
boolean excepted = false;
try {
GWASData data = parser.parse();
} catch (ParserException e) {
excepted = true;
}
assertTrue(excepted);
}
@Test
public void testLoadGWAS() throws Exception{
ResourceLocator locator = new ResourceLocator(TestUtils.DATA_DIR + "gwas/smallp.gwas");
List<Track> tracks = (new TrackLoader()).load(locator, genome);
GWASTrack track = (GWASTrack) tracks.get(0);
String desc = track.getDescription("chr6", 1);
String[] lines = desc.split("<br>");
String[] expTokens = new String[]{"rs29228", "6", "29623739", "0.931148124684"};
int offset = 3;
for(int tn=0; tn < expTokens.length; tn++){
String token = lines[tn+offset];
String[] areas = token.split("\\s");
String value = areas[1];
assertEquals("Value for field " + areas[0] + " not equal", expTokens[tn], value);
}
}
}