tests for read count and rpkm calculations

test/uk/ac/sanger/artemis/components/alignment/MappedReadsTest.java

+/* 
+ * 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);
+  }
+}