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