From 7b7a4876dd7cf2021dda457047653c87a9e85fa0 Mon Sep 17 00:00:00 2001
From: tcarver <tjc>
Date: Tue, 11 Mar 2014 16:39:38 +0000
Subject: [PATCH] tests for read count and rpkm calculations
---
.../components/alignment/MappedReadsTest.java | 143 ++++++++++++++++++
1 file changed, 143 insertions(+)
create mode 100644 test/uk/ac/sanger/artemis/components/alignment/MappedReadsTest.java
diff --git a/test/uk/ac/sanger/artemis/components/alignment/MappedReadsTest.java b/test/uk/ac/sanger/artemis/components/alignment/MappedReadsTest.java
new file mode 100644
index 000000000..976053479
--- /dev/null
+++ b/test/uk/ac/sanger/artemis/components/alignment/MappedReadsTest.java
@@ -0,0 +1,143 @@
+/*
+ * 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);
+ }
+}
--
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