test/jalview/ext/ensembl/EnsemblGenomeTest.java

   1 package jalview.ext.ensembl;
   2
   3 import static org.testng.AssertJUnit.assertEquals;
   4 import static org.testng.AssertJUnit.assertFalse;
   5 import static org.testng.AssertJUnit.assertTrue;
   6
   7 import jalview.datamodel.SequenceDummy;
   8 import jalview.datamodel.SequenceFeature;
   9 import jalview.datamodel.SequenceI;
  10 import jalview.io.gff.SequenceOntologyFactory;
  11 import jalview.io.gff.SequenceOntologyLite;
  12 import jalview.util.MapList;
  13
  14 import java.util.List;
  15
  16 import org.testng.annotations.AfterClass;
  17 import org.testng.annotations.BeforeClass;
  18 import org.testng.annotations.Test;
  19
  20 public class EnsemblGenomeTest
  21 {
  22   @BeforeClass(alwaysRun = true)
  23   public void setUp()
  24   {
  25     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
  26   }
  27
  28   @AfterClass(alwaysRun = true)
  29   public void tearDown()
  30   {
  31     SequenceOntologyFactory.setInstance(null);
  32   }
  33
  34   /**
  35    * Test that the genomic sequence part of genomic sequence is correctly
  36    * identified by 'transcript' features (or subtypes) with the correct gene ID
  37    */
  38   @Test(groups = "Functional")
  39   public void testGetGenomicRangesFromFeatures()
  40   {
  41     EnsemblGenome testee = new EnsemblGenome();
  42     SequenceI genomic = new SequenceDummy("chr7");
  43     genomic.setStart(10000);
  44     genomic.setEnd(50000);
  45     String transcriptId = "ABC123";
  46
  47     // transcript at (start+10000) length 501
  48     SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
  49             20500, 0f, null);
  50     sf.setValue("ID", "transcript:" + transcriptId);
  51     sf.setStrand("+");
  52     genomic.addSequenceFeature(sf);
  53
  54     // transcript (sub-type) at (start + 10500) length 101
  55     sf = new SequenceFeature("ncRNA", "", 10500, 10600, 0f, null);
  56     sf.setValue("ID", "transcript:" + transcriptId);
  57     sf.setStrand("+");
  58     genomic.addSequenceFeature(sf);
  59
  60     // Ensembl treats NMD_transcript_variant as if transcript
  61     // although strictly it is a sequence_variant in SO
  62     sf = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000,
  63             0f, null);
  64     sf.setValue("ID", "transcript:" + transcriptId);
  65     sf.setStrand("+");
  66     genomic.addSequenceFeature(sf);
  67
  68     // transcript with a different ID doesn't count
  69     sf = new SequenceFeature("transcript", "", 11500, 12600, 0f, null);
  70     sf.setValue("ID", "transcript:anotherOne");
  71     genomic.addSequenceFeature(sf);
  72
  73     // parent of transcript feature doesn't count
  74     sf = new SequenceFeature("gene_member_region", "", 10000, 50000, 0f,
  75             null);
  76     genomic.addSequenceFeature(sf);
  77
  78     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
  79             transcriptId, 23);
  80     List<int[]> fromRanges = ranges.getFromRanges();
  81     assertEquals(3, fromRanges.size());
  82     // from ranges should be sorted by start order
  83     assertEquals(10500, fromRanges.get(0)[0]);
  84     assertEquals(10600, fromRanges.get(0)[1]);
  85     assertEquals(11000, fromRanges.get(1)[0]);
  86     assertEquals(12000, fromRanges.get(1)[1]);
  87     assertEquals(20000, fromRanges.get(2)[0]);
  88     assertEquals(20500, fromRanges.get(2)[1]);
  89     // to range should start from given start numbering
  90     List<int[]> toRanges = ranges.getToRanges();
  91     assertEquals(1, toRanges.size());
  92     assertEquals(23, toRanges.get(0)[0]);
  93     assertEquals(1625, toRanges.get(0)[1]);
  94   }
  95
  96   /**
  97    * Test the method that retains features except for 'transcript' (or
  98    * sub-type), or those with parent other than the given id
  99    */
 100   @Test(groups = "Functional")
 101   public void testRetainFeature()
 102   {
 103     String accId = "ABC123";
 104     EnsemblGenome testee = new EnsemblGenome();
 105
 106     SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
 107             20500, 0f, null);
 108     assertFalse(testee.retainFeature(sf, accId));
 109
 110     sf.setType("mature_transcript");
 111     assertFalse(testee.retainFeature(sf, accId));
 112
 113     sf.setType("NMD_transcript_variant");
 114     assertFalse(testee.retainFeature(sf, accId));
 115
 116     // other feature with no parent is kept
 117     sf.setType("anything");
 118     assertTrue(testee.retainFeature(sf, accId));
 119
 120     // other feature with correct parent is kept
 121     sf.setValue("Parent", "transcript:" + accId);
 122     assertTrue(testee.retainFeature(sf, accId));
 123
 124     // other feature with wrong parent is not kept
 125     sf.setValue("Parent", "transcript:XYZ");
 126     assertFalse(testee.retainFeature(sf, accId));
 127   }
 128
 129   /**
 130    * Test the method that picks out 'transcript' (or subtype) features with the
 131    * accession id as ID
 132    */
 133   @Test(groups = "Functional")
 134   public void testIdentifiesSequence()
 135   {
 136     String accId = "ABC123";
 137     EnsemblGenome testee = new EnsemblGenome();
 138
 139     // transcript with no ID not valid
 140     SequenceFeature sf = new SequenceFeature("transcript", "", 1, 2, 0f,
 141             null);
 142     assertFalse(testee.identifiesSequence(sf, accId));
 143
 144     // transcript with wrong ID not valid
 145     sf.setValue("ID", "transcript");
 146     assertFalse(testee.identifiesSequence(sf, accId));
 147
 148     // transcript with right ID is valid
 149     sf.setValue("ID", "transcript:" + accId);
 150     assertTrue(testee.identifiesSequence(sf, accId));
 151
 152     // transcript sub-type with right ID is valid
 153     sf.setType("ncRNA");
 154     assertTrue(testee.identifiesSequence(sf, accId));
 155
 156     // Ensembl treats NMD_transcript_variant as if a transcript
 157     sf.setType("NMD_transcript_variant");
 158     assertTrue(testee.identifiesSequence(sf, accId));
 159
 160     // gene not valid:
 161     sf.setType("gene");
 162     assertFalse(testee.identifiesSequence(sf, accId));
 163
 164     // exon not valid:
 165     sf.setType("exon");
 166     assertFalse(testee.identifiesSequence(sf, accId));
 167   }
 168
 169 }