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,
  50             null);
  51     sf.setValue("ID", "transcript:" + transcriptId);
  52     sf.setStrand("+");
  53     genomic.addSequenceFeature(sf);
  54
  55     // transcript (sub-type) at (start + 10500) length 101
  56     sf = new SequenceFeature("ncRNA", "", 10500, 10600, 0f, null);
  57     sf.setValue("ID", "transcript:" + transcriptId);
  58     sf.setStrand("+");
  59     genomic.addSequenceFeature(sf);
  60
  61     // Ensembl treats NMD_transcript_variant as if transcript
  62     // although strictly it is a sequence_variant in SO
  63     sf = new SequenceFeature("NMD_transcript_variant", "", 11000, 12000,
  64             0f, null);
  65     sf.setValue("ID", "transcript:" + transcriptId);
  66     sf.setStrand("+");
  67     genomic.addSequenceFeature(sf);
  68
  69     // transcript with a different ID doesn't count
  70     sf = new SequenceFeature("transcript", "", 11500, 12600, 0f, null);
  71     sf.setValue("ID", "transcript:anotherOne");
  72     genomic.addSequenceFeature(sf);
  73
  74     // parent of transcript feature doesn't count
  75     sf = new SequenceFeature("gene_member_region", "", 10000, 50000, 0f,
  76             null);
  77     genomic.addSequenceFeature(sf);
  78
  79     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
  80             transcriptId, 23);
  81     List<int[]> fromRanges = ranges.getFromRanges();
  82     assertEquals(3, fromRanges.size());
  83     // from ranges should be sorted by start order
  84     assertEquals(10500, fromRanges.get(0)[0]);
  85     assertEquals(10600, fromRanges.get(0)[1]);
  86     assertEquals(11000, fromRanges.get(1)[0]);
  87     assertEquals(12000, fromRanges.get(1)[1]);
  88     assertEquals(20000, fromRanges.get(2)[0]);
  89     assertEquals(20500, fromRanges.get(2)[1]);
  90     // to range should start from given start numbering
  91     List<int[]> toRanges = ranges.getToRanges();
  92     assertEquals(1, toRanges.size());
  93     assertEquals(23, toRanges.get(0)[0]);
  94     assertEquals(1625, toRanges.get(0)[1]);
  95   }
  96
  97   /**
  98    * Test the method that retains features except for 'transcript' (or
  99    * sub-type), or those with parent other than the given id
 100    */
 101   @Test(groups = "Functional")
 102   public void testRetainFeature()
 103   {
 104     String accId = "ABC123";
 105     EnsemblGenome testee = new EnsemblGenome();
 106
 107     SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
 108             20500, 0f, null);
 109     assertFalse(testee.retainFeature(sf, accId));
 110
 111     sf.setType("mature_transcript");
 112     assertFalse(testee.retainFeature(sf, accId));
 113
 114     sf.setType("NMD_transcript_variant");
 115     assertFalse(testee.retainFeature(sf, accId));
 116
 117     // other feature with no parent is kept
 118     sf.setType("anything");
 119     assertTrue(testee.retainFeature(sf, accId));
 120
 121     // other feature with correct parent is kept
 122     sf.setValue("Parent", "transcript:" + accId);
 123     assertTrue(testee.retainFeature(sf, accId));
 124
 125     // other feature with wrong parent is not kept
 126     sf.setValue("Parent", "transcript:XYZ");
 127     assertFalse(testee.retainFeature(sf, accId));
 128   }
 129
 130   /**
 131    * Test the method that picks out 'transcript' (or subtype) features with the
 132    * accession id as ID
 133    */
 134   @Test(groups = "Functional")
 135   public void testIdentifiesSequence()
 136   {
 137     String accId = "ABC123";
 138     EnsemblGenome testee = new EnsemblGenome();
 139
 140     // transcript with no ID not valid
 141     SequenceFeature sf = new SequenceFeature("transcript", "", 1, 2, 0f,
 142             null);
 143     assertFalse(testee.identifiesSequence(sf, accId));
 144
 145     // transcript with wrong ID not valid
 146     sf.setValue("ID", "transcript");
 147     assertFalse(testee.identifiesSequence(sf, accId));
 148
 149     // transcript with right ID is valid
 150     sf.setValue("ID", "transcript:" + accId);
 151     assertTrue(testee.identifiesSequence(sf, accId));
 152
 153     // transcript sub-type with right ID is valid
 154     sf.setType("ncRNA");
 155     assertTrue(testee.identifiesSequence(sf, accId));
 156
 157     // Ensembl treats NMD_transcript_variant as if a transcript
 158     sf.setType("NMD_transcript_variant");
 159     assertTrue(testee.identifiesSequence(sf, accId));
 160
 161     // gene not valid:
 162     sf.setType("gene");
 163     assertFalse(testee.identifiesSequence(sf, accId));
 164
 165     // exon not valid:
 166     sf.setType("exon");
 167     assertFalse(testee.identifiesSequence(sf, accId));
 168   }
 169
 170 }