test/jalview/ext/ensembl/EnsemblGeneTest.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.assertSame;
   6 import static org.testng.AssertJUnit.assertTrue;
   7
   8 import jalview.api.FeatureSettingsModelI;
   9 import jalview.datamodel.SequenceDummy;
  10 import jalview.datamodel.SequenceFeature;
  11 import jalview.datamodel.SequenceI;
  12 import jalview.io.gff.SequenceOntologyFactory;
  13 import jalview.io.gff.SequenceOntologyLite;
  14 import jalview.util.MapList;
  15
  16 import java.awt.Color;
  17 import java.util.List;
  18
  19 import org.testng.annotations.AfterClass;
  20 import org.testng.annotations.BeforeClass;
  21 import org.testng.annotations.Test;
  22
  23 public class EnsemblGeneTest
  24 {
  25   @BeforeClass(alwaysRun = true)
  26   public void setUp()
  27   {
  28     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
  29   }
  30
  31   @AfterClass(alwaysRun = true)
  32   public void tearDown()
  33   {
  34     SequenceOntologyFactory.setInstance(null);
  35   }
  36
  37   /**
  38    * Test that the gene part of genomic sequence is uniquely identified by a
  39    * 'gene' features (or subtype) with the correct gene ID
  40    */
  41   @Test(groups = "Functional")
  42   public void testGetGenomicRangesFromFeatures()
  43   {
  44     EnsemblGene testee = new EnsemblGene();
  45     SequenceI genomic = new SequenceDummy("chr7");
  46     genomic.setStart(10000);
  47     genomic.setEnd(50000);
  48     String geneId = "ABC123";
  49
  50     // gene at (start+10000) length 501
  51     SequenceFeature sf = new SequenceFeature("gene", "", 20000, 20500, 0f,
  52             null);
  53     sf.setValue("ID", "gene:" + geneId);
  54     sf.setStrand("+");
  55     genomic.addSequenceFeature(sf);
  56
  57     // gene at (start + 10500) length 101
  58     // should be ignored - the first 'gene' found defines the whole range
  59     sf = new SequenceFeature("gene", "", 10500, 10600, 0f, null);
  60     sf.setValue("ID", "gene:" + geneId);
  61     sf.setStrand("+");
  62     genomic.addSequenceFeature(sf);
  63
  64     MapList ranges = testee.getGenomicRangesFromFeatures(genomic, geneId,
  65             23);
  66     List<int[]> fromRanges = ranges.getFromRanges();
  67     assertEquals(1, fromRanges.size());
  68     assertEquals(20000, fromRanges.get(0)[0]);
  69     assertEquals(20500, fromRanges.get(0)[1]);
  70     // to range should start from given start numbering
  71     List<int[]> toRanges = ranges.getToRanges();
  72     assertEquals(1, toRanges.size());
  73     assertEquals(23, toRanges.get(0)[0]);
  74     assertEquals(523, toRanges.get(0)[1]);
  75   }
  76
  77   /**
  78    * Test variant using a sub-type of gene from the Sequence Ontology
  79    */
  80   @Test(groups = "Functional")
  81   public void testGetGenomicRangesFromFeatures_ncRNA_gene_reverseStrand()
  82   {
  83     EnsemblGene testee = new EnsemblGene();
  84     SequenceI genomic = new SequenceDummy("chr7");
  85     genomic.setStart(10000);
  86     genomic.setEnd(50000);
  87     String geneId = "ABC123";
  88
  89     // gene at (start+10000) length 501
  90     SequenceFeature sf = new SequenceFeature("ncRNA_gene", "", 20000,
  91             20500, 0f, null);
  92     sf.setValue("ID", "gene:" + geneId);
  93     sf.setStrand("-");
  94     genomic.addSequenceFeature(sf);
  95
  96     // gene at (start + 10500) length 101
  97     // should be ignored - the first 'gene' found defines the whole range
  98     // (real data would only have one such feature)
  99     sf = new SequenceFeature("gene", "", 10500, 10600, 0f, null);
 100     sf.setValue("ID", "gene:" + geneId);
 101     sf.setStrand("+");
 102     genomic.addSequenceFeature(sf);
 103
 104     MapList ranges = testee.getGenomicRangesFromFeatures(genomic, geneId,
 105             23);
 106     List<int[]> fromRanges = ranges.getFromRanges();
 107     assertEquals(1, fromRanges.size());
 108     // from range on reverse strand:
 109     assertEquals(20500, fromRanges.get(0)[0]);
 110     assertEquals(20000, fromRanges.get(0)[1]);
 111     // to range should start from given start numbering
 112     List<int[]> toRanges = ranges.getToRanges();
 113     assertEquals(1, toRanges.size());
 114     assertEquals(23, toRanges.get(0)[0]);
 115     assertEquals(523, toRanges.get(0)[1]);
 116   }
 117
 118   /**
 119    * Test the method that extracts transcript (or subtype) features with a
 120    * specified gene as parent
 121    */
 122   @Test(groups = "Functional")
 123   public void testGetTranscriptFeatures()
 124   {
 125     SequenceI genomic = new SequenceDummy("chr7");
 126     genomic.setStart(10000);
 127     genomic.setEnd(50000);
 128     String geneId = "ABC123";
 129
 130     // transcript feature
 131     SequenceFeature sf1 = new SequenceFeature("transcript", "", 20000,
 132             20500, 0f, null);
 133     sf1.setValue("Parent", "gene:" + geneId);
 134     sf1.setValue("transcript_id", "transcript1");
 135     genomic.addSequenceFeature(sf1);
 136
 137     // transcript sub-type feature
 138     SequenceFeature sf2 = new SequenceFeature("snRNA", "", 20000,
 139             20500, 0f, null);
 140     sf2.setValue("Parent", "gene:" + geneId);
 141     sf2.setValue("transcript_id", "transcript2");
 142     genomic.addSequenceFeature(sf2);
 143
 144     // NMD_transcript_variant treated like transcript in Ensembl
 145     SequenceFeature sf3 = new SequenceFeature("NMD_transcript_variant", "",
 146             20000, 20500, 0f, null);
 147     sf3.setValue("Parent", "gene:" + geneId);
 148     sf3.setValue("transcript_id", "transcript3");
 149     genomic.addSequenceFeature(sf3);
 150
 151     // transcript for a different gene - ignored
 152     SequenceFeature sf4 = new SequenceFeature("snRNA", "", 20000, 20500,
 153             0f, null);
 154     sf4.setValue("Parent", "gene:XYZ");
 155     sf4.setValue("transcript_id", "transcript4");
 156     genomic.addSequenceFeature(sf4);
 157
 158     EnsemblGene testee = new EnsemblGene();
 159
 160     /*
 161      * with no filter
 162      */
 163     List<SequenceFeature> features = testee.getTranscriptFeatures(geneId,
 164             genomic);
 165     assertEquals(3, features.size());
 166     assertSame(sf1, features.get(0));
 167     assertSame(sf2, features.get(1));
 168     assertSame(sf3, features.get(2));
 169   }
 170
 171   /**
 172    * Test the method that retains features except for 'gene', or 'transcript'
 173    * with parent other than the given id
 174    */
 175   @Test(groups = "Functional")
 176   public void testRetainFeature()
 177   {
 178     String geneId = "ABC123";
 179     EnsemblGene testee = new EnsemblGene();
 180     SequenceFeature sf = new SequenceFeature("gene", "", 20000,
 181             20500, 0f, null);
 182     sf.setValue("ID", "gene:" + geneId);
 183     assertFalse(testee.retainFeature(sf, geneId));
 184
 185     sf.setType("transcript");
 186     sf.setValue("Parent", "gene:" + geneId);
 187     assertTrue(testee.retainFeature(sf, geneId));
 188
 189     sf.setType("mature_transcript");
 190     sf.setValue("Parent", "gene:" + geneId);
 191     assertTrue(testee.retainFeature(sf, geneId));
 192
 193     sf.setType("NMD_transcript_variant");
 194     sf.setValue("Parent", "gene:" + geneId);
 195     assertTrue(testee.retainFeature(sf, geneId));
 196
 197     sf.setValue("Parent", "gene:XYZ");
 198     assertFalse(testee.retainFeature(sf, geneId));
 199
 200     sf.setType("anything");
 201     assertTrue(testee.retainFeature(sf, geneId));
 202   }
 203
 204   /**
 205    * Test the method that picks out 'gene' (or subtype) features with the
 206    * accession id as ID
 207    */
 208   @Test(groups = "Functional")
 209   public void testIdentifiesSequence()
 210   {
 211     String accId = "ABC123";
 212     EnsemblGene testee = new EnsemblGene();
 213
 214     // gene with no ID not valid
 215     SequenceFeature sf = new SequenceFeature("gene", "", 1, 2, 0f, null);
 216     assertFalse(testee.identifiesSequence(sf, accId));
 217
 218     // gene with wrong ID not valid
 219     sf.setValue("ID", "gene:XYZ");
 220     assertFalse(testee.identifiesSequence(sf, accId));
 221
 222     // gene with right ID is valid
 223     sf.setValue("ID", "gene:" + accId);
 224     assertTrue(testee.identifiesSequence(sf, accId));
 225
 226     // gene sub-type with right ID is valid
 227     sf.setType("snRNA_gene");
 228     assertTrue(testee.identifiesSequence(sf, accId));
 229
 230     // transcript not valid:
 231     sf.setType("transcript");
 232     assertFalse(testee.identifiesSequence(sf, accId));
 233
 234     // exon not valid:
 235     sf.setType("exon");
 236     assertFalse(testee.identifiesSequence(sf, accId));
 237   }
 238
 239   /**
 240    * Check behaviour of feature colour scheme for EnsemblGene sequences.
 241    * Currently coded to display exon and sequence_variant (or sub-types) only,
 242    * with sequence_variant in red above exon coloured by label.
 243    */
 244   @Test(groups = "Functional")
 245   public void testGetFeatureColourScheme()
 246   {
 247     FeatureSettingsModelI fc = new EnsemblGene().getFeatureColourScheme();
 248     assertTrue(fc.isFeatureDisplayed("exon"));
 249     assertTrue(fc.isFeatureDisplayed("coding_exon")); // subtype of exon
 250     assertTrue(fc.isFeatureDisplayed("sequence_variant"));
 251     assertTrue(fc.isFeatureDisplayed("feature_variant")); // subtype
 252     assertFalse(fc.isFeatureDisplayed("transcript"));
 253     assertEquals(Color.RED, fc.getFeatureColour("sequence_variant")
 254             .getColour());
 255     assertEquals(Color.RED, fc.getFeatureColour("feature_variant")
 256             .getColour());
 257     assertTrue(fc.getFeatureColour("exon").isColourByLabel());
 258     assertTrue(fc.getFeatureColour("coding_exon").isColourByLabel());
 259     assertEquals(1, fc.compare("sequence_variant", "exon"));
 260     assertEquals(-1, fc.compare("exon", "sequence_variant"));
 261     assertEquals(1, fc.compare("feature_variant", "coding_exon"));
 262     assertEquals(-1, fc.compare("coding_exon", "feature_variant"));
 263     assertEquals(1f, fc.getTransparency());
 264   }
 265 }