test/jalview/ext/ensembl/EnsemblGenomeTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.ext.ensembl;
  22
  23 import static org.testng.AssertJUnit.assertEquals;
  24 import static org.testng.AssertJUnit.assertFalse;
  25 import static org.testng.AssertJUnit.assertTrue;
  26
  27 import jalview.datamodel.Sequence;
  28 import jalview.datamodel.SequenceDummy;
  29 import jalview.datamodel.SequenceFeature;
  30 import jalview.datamodel.SequenceI;
  31 import jalview.gui.JvOptionPane;
  32 import jalview.io.gff.SequenceOntologyFactory;
  33 import jalview.io.gff.SequenceOntologyLite;
  34 import jalview.util.MapList;
  35
  36 import java.util.List;
  37
  38 import org.testng.annotations.AfterClass;
  39 import org.testng.annotations.BeforeClass;
  40 import org.testng.annotations.Test;
  41
  42 public class EnsemblGenomeTest
  43 {
  44
  45   @BeforeClass(alwaysRun = true)
  46   public void setUpJvOptionPane()
  47   {
  48     JvOptionPane.setInteractiveMode(false);
  49     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  50   }
  51
  52   @BeforeClass(alwaysRun = true)
  53   public void setUp()
  54   {
  55     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
  56   }
  57
  58   @AfterClass(alwaysRun = true)
  59   public void tearDown()
  60   {
  61     SequenceOntologyFactory.setInstance(null);
  62   }
  63
  64   /**
  65    * Test that the genomic sequence part of genomic sequence is correctly
  66    * identified by 'transcript' features (or subtypes) with the correct gene ID
  67    */
  68   @Test(groups = "Functional")
  69   public void testGetGenomicRangesFromFeatures()
  70   {
  71     EnsemblGenome testee = new EnsemblGenome();
  72     SequenceI genomic = new SequenceDummy("chr7");
  73     genomic.setStart(10000);
  74     genomic.setEnd(50000);
  75     String transcriptId = "ABC123";
  76
  77     // transcript at (start+10000) length 501
  78     SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
  79             20500, 0f, null);
  80     sf.setValue("ID", "transcript:" + transcriptId);
  81     sf.setStrand("+");
  82     genomic.addSequenceFeature(sf);
  83
  84     // transcript (sub-type) at (start + 10500) length 101
  85     sf = new SequenceFeature("ncRNA", "", 10500, 10600, 0f, null);
  86     sf.setValue("ID", "transcript:" + transcriptId);
  87     sf.setStrand("+");
  88     genomic.addSequenceFeature(sf);
  89
  90     // Ensembl treats NMD_transcript_variant as if transcript
  91     // although strictly it is a sequence_variant in SO
  92     sf = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000,
  93             0f, null);
  94     sf.setValue("ID", "transcript:" + transcriptId);
  95     sf.setStrand("+");
  96     genomic.addSequenceFeature(sf);
  97
  98     // transcript with a different ID doesn't count
  99     sf = new SequenceFeature("transcript", "", 11500, 12600, 0f, null);
 100     sf.setValue("ID", "transcript:anotherOne");
 101     genomic.addSequenceFeature(sf);
 102
 103     // parent of transcript feature doesn't count
 104     sf = new SequenceFeature("gene_member_region", "", 10000, 50000, 0f,
 105             null);
 106     genomic.addSequenceFeature(sf);
 107
 108     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
 109             transcriptId, 23);
 110     List<int[]> fromRanges = ranges.getFromRanges();
 111     assertEquals(3, fromRanges.size());
 112     // from ranges should be sorted by start order
 113     assertEquals(10500, fromRanges.get(0)[0]);
 114     assertEquals(10600, fromRanges.get(0)[1]);
 115     assertEquals(11000, fromRanges.get(1)[0]);
 116     assertEquals(12000, fromRanges.get(1)[1]);
 117     assertEquals(20000, fromRanges.get(2)[0]);
 118     assertEquals(20500, fromRanges.get(2)[1]);
 119     // to range should start from given start numbering
 120     List<int[]> toRanges = ranges.getToRanges();
 121     assertEquals(1, toRanges.size());
 122     assertEquals(23, toRanges.get(0)[0]);
 123     assertEquals(1625, toRanges.get(0)[1]);
 124   }
 125
 126   /**
 127    * Test the method that retains features except for 'transcript' (or
 128    * sub-type), or those with parent other than the given id
 129    */
 130   @Test(groups = "Functional")
 131   public void testRetainFeature()
 132   {
 133     String accId = "ABC123";
 134     EnsemblGenome testee = new EnsemblGenome();
 135
 136     SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
 137             20500, 0f, null);
 138     assertFalse(testee.retainFeature(sf, accId));
 139
 140     sf = new SequenceFeature("mature_transcript", "", 20000, 20500, 0f,
 141             null);
 142     assertFalse(testee.retainFeature(sf, accId));
 143
 144     sf = new SequenceFeature("NMD_transcript_variant", "", 20000, 20500,
 145             0f, null);
 146     assertFalse(testee.retainFeature(sf, accId));
 147
 148     // other feature with no parent is kept
 149     sf = new SequenceFeature("anything", "", 20000, 20500, 0f, null);
 150     assertTrue(testee.retainFeature(sf, accId));
 151
 152     // other feature with correct parent is kept
 153     sf.setValue("Parent", "transcript:" + accId);
 154     assertTrue(testee.retainFeature(sf, accId));
 155
 156     // other feature with wrong parent is not kept
 157     sf.setValue("Parent", "transcript:XYZ");
 158     assertFalse(testee.retainFeature(sf, accId));
 159   }
 160
 161   /**
 162    * Test the method that picks out 'transcript' (or subtype) features with the
 163    * accession id as ID
 164    */
 165   @Test(groups = "Functional")
 166   public void testGetIdentifyingFeatures()
 167   {
 168     String accId = "ABC123";
 169     SequenceI seq = new Sequence(accId, "HEARTS");
 170
 171     // transcript with no ID not valid
 172     SequenceFeature sf1 = new SequenceFeature("transcript", "", 1, 2, 0f,
 173             null);
 174     seq.addSequenceFeature(sf1);
 175
 176     // transcript with wrong ID not valid
 177     SequenceFeature sf2 = new SequenceFeature("transcript", "", 1, 2, 0f,
 178             null);
 179     sf2.setValue("ID", "transcript");
 180     seq.addSequenceFeature(sf2);
 181
 182     // transcript with right ID is valid
 183     SequenceFeature sf3 = new SequenceFeature("transcript", "", 1, 2, 0f,
 184             null);
 185     sf3.setValue("ID", "transcript:" + accId);
 186     seq.addSequenceFeature(sf3);
 187
 188     // transcript sub-type with right ID is valid
 189     SequenceFeature sf4 = new SequenceFeature("ncRNA", "", 1, 2, 0f, null);
 190     sf4.setValue("ID", "transcript:" + accId);
 191     seq.addSequenceFeature(sf4);
 192
 193     // Ensembl treats NMD_transcript_variant as if a transcript
 194     SequenceFeature sf5 = new SequenceFeature("NMD_transcript_variant", "",
 195             1, 2, 0f, null);
 196     sf5.setValue("ID", "transcript:" + accId);
 197     seq.addSequenceFeature(sf5);
 198
 199     // gene not valid:
 200     SequenceFeature sf6 = new SequenceFeature("gene", "", 1, 2, 0f, null);
 201     sf6.setValue("ID", "transcript:" + accId);
 202     seq.addSequenceFeature(sf6);
 203
 204     // exon not valid:
 205     SequenceFeature sf7 = new SequenceFeature("exon", "", 1, 2, 0f, null);
 206     sf7.setValue("ID", "transcript:" + accId);
 207     seq.addSequenceFeature(sf7);
 208
 209     List<SequenceFeature> sfs = new EnsemblGenome()
 210             .getIdentifyingFeatures(seq, accId);
 211     assertFalse(sfs.contains(sf1));
 212     assertFalse(sfs.contains(sf2));
 213     assertTrue(sfs.contains(sf3));
 214     assertTrue(sfs.contains(sf4));
 215     assertTrue(sfs.contains(sf5));
 216     assertFalse(sfs.contains(sf6));
 217     assertFalse(sfs.contains(sf7));
 218   }
 219
 220 }