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/*
* This file is part of Artemis
*
* Copyright (C) 2014 Genome Research Limited
*
* This program is free software; you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation; either version 2
* of the License, or (at your option) any later version.
*
* This program is distributed in the hope that it will be useful,
* but WITHOUT ANY WARRANTY; without even the implied warranty of
* MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
* GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with this program; if not, write to the Free Software
* Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
*
*/
package uk.ac.sanger.artemis.components.alignment;
import static org.junit.Assert.assertTrue;
import java.awt.GraphicsEnvironment;
import java.net.URL;
import java.util.Hashtable;
import java.util.List;
import javax.swing.JFrame;
import junit.framework.Assert;
import uk.ac.sanger.artemis.io.Utils;
import org.junit.BeforeClass;
import org.junit.Test;
import uk.ac.sanger.artemis.EntryGroup;
import uk.ac.sanger.artemis.Feature;
import uk.ac.sanger.artemis.FeatureVector;
import uk.ac.sanger.artemis.components.EntryEdit;
import uk.ac.sanger.artemis.components.alignment.BamUtils;
import uk.ac.sanger.artemis.components.alignment.BamView;
import uk.ac.sanger.artemis.components.alignment.MappedReads;
import uk.ac.sanger.artemis.components.alignment.ReadCount;
public class MappedReadsTest
{
private static BamView bv;
private static FeatureVector fv;
@BeforeClass
public static void setUp()
{
// ignore if in headless mode with no x11
if(GraphicsEnvironment.getLocalGraphicsEnvironment().isHeadless())
return;
URL entryFile = MappedReadsTest.class.getResource("/data/MAL_8h.bam");
System.setProperty("bam", entryFile.getFile());
final EntryGroup egrp = Utils.getEntryGroup("/data/MAL1.embl.gz");
final EntryEdit ee = new EntryEdit(egrp);
ee.setVisible(true);
while( (bv = ee.getJamView()) == null)
{
// wait for BamView to be constructed
try {
Thread.sleep(100);
} catch(Exception e){};
}
// get a gene feature
fv = new FeatureVector();
final FeatureVector features = egrp.getAllFeatures();
for(int i=0; i<features.size(); i++)
{
Feature f = features.elementAt(i);
if(f.getSystematicName().equals("PFA0110w"))
fv.add(f);
}
}
@Test
/**
* Test the read count for a gene
*/
public void readCounts()
{
// ignore if in headless mode with no x11
if(GraphicsEnvironment.getLocalGraphicsEnvironment().isHeadless())
return;
final Hashtable<String, List<ReadCount>> featureReadCount =
BamUtils.calculateMappedReads(bv, fv, false, true, false, null, null);
final List<ReadCount> cnts = featureReadCount.get("PFA0110w");
ReadCount c = cnts.get(0);
assertTrue(2153.f == c.senseCnt);
assertTrue(1443.f == c.antiCnt);
}
@Test
/**
* Read count for a gene excluding the intron
*/
public void readCountsExcludeIntron()
{
// ignore if in headless mode with no x11
if(GraphicsEnvironment.getLocalGraphicsEnvironment().isHeadless())
return;
final Hashtable<String, List<ReadCount>> featureReadCount =
BamUtils.calculateMappedReads(bv, fv, false, false, false, null, null);
final List<ReadCount> cnts = featureReadCount.get("PFA0110w");
ReadCount c = cnts.get(0);
assertTrue(2152.f == c.senseCnt);
assertTrue(1442.f == c.antiCnt);
}
@Test
/**
* Tes the read count for a gene not including those in the intron
*/
public void rpkm()
{
// ignore if in headless mode with no x11
if(GraphicsEnvironment.getLocalGraphicsEnvironment().isHeadless())
return;
String refName = (String) bv.getCombo().getSelectedItem();
int thisLength = bv.getSeqLengths().get(refName);
int mappedReads[] = BamUtils.calc(bv, refName, thisLength,
false, null);
Hashtable<String, List<ReadCount>> featureReadCount =
BamUtils.calculateMappedReads(bv, fv, false, true, false, mappedReads, null);
final List<ReadCount> cnts = featureReadCount.get("PFA0110w");
ReadCount c = cnts.get(0);
assertTrue(183514.266f == c.senseCnt);
assertTrue(122996.328f == c.antiCnt);
}
}