test/jalview/datamodel/ontology/OntologyBaseTest.java

   1 package jalview.datamodel.ontology;
   2
   3 import static org.testng.Assert.assertEquals;
   4 import static org.testng.Assert.assertTrue;
   5
   6 import jalview.ext.so.SequenceOntology;
   7 import jalview.io.gff.SequenceOntologyFactory;
   8
   9 import java.util.Arrays;
  10 import java.util.List;
  11 import java.util.Map;
  12
  13 import org.testng.annotations.AfterClass;
  14 import org.testng.annotations.BeforeClass;
  15 import org.testng.annotations.Test;
  16
  17 public class OntologyBaseTest
  18 {
  19   @BeforeClass(alwaysRun = true)
  20   public void setUp()
  21   {
  22     SequenceOntologyFactory.setInstance(new SequenceOntology());
  23   }
  24
  25   @AfterClass(alwaysRun = true)
  26   public void tearDown()
  27   {
  28     SequenceOntologyFactory.setInstance(null);
  29   }
  30
  31   @Test(groups = "Functional")
  32   public void testfindSequenceOntologyGroupings()
  33   {
  34     /*
  35      * typical gnomAD feature types, plus the top level 'sequence_variant' as in dbSNP
  36      */
  37     List<String> featureTypes = Arrays.asList("sequence_variant",
  38             "inframe_insertion", "stop_lost", "stop_gained",
  39             "5_prime_UTR_variant", "non_coding_transcript_exon_variant",
  40             "synonymous_variant", "inframe_deletion", "frameshift_variant",
  41             "upstream_gene_variant", "splice_region_variant",
  42             "missense_variant");
  43
  44     /*
  45      * for stop_gained:
  46      * transcript_variant further adds 5_prime_UTR_variant,
  47      *     non_coding_transcript_exon_variant, synonymous_variant, splice_region_variant
  48      * feature_variant further adds upstream_gene_variant
  49      * sequence_variant further adds sequence_variant
  50      */
  51     Map<String, List<String>> map = SequenceOntologyFactory.getInstance()
  52             .findSequenceOntologyGroupings("stop_gained", featureTypes);
  53     assertEquals(map.size(), 10);
  54
  55     /*
  56      * feature_truncation adds inframe_deletion
  57      */
  58     List<String> terms = map.get("feature_truncation");
  59     assertEquals(terms.size(), 1);
  60     assertTrue(terms.contains("inframe_deletion"));
  61
  62     /*
  63      * nonsynonymous_variant adds stop_lost, missense_variant
  64      */
  65     terms = map.get("nonsynonymous_variant");
  66     assertEquals(terms.size(), 2);
  67     assertEquals(terms.toString(), "[missense_variant, stop_lost]");
  68
  69     /*
  70      * inframe_variant further adds inframe_deletion, inframe_insertion
  71      */
  72     terms = map.get("inframe_variant");
  73     assertEquals(terms.size(), 4);
  74     assertEquals(terms.toString(),
  75             "[inframe_deletion, inframe_insertion, missense_variant, stop_lost]");
  76
  77     /*
  78      * protein_altering_variant further adds frameshift_variant
  79      */
  80     terms = map.get("protein_altering_variant");
  81     assertEquals(terms.size(), 5);
  82     assertEquals(terms.toString(),
  83             "[frameshift_variant, inframe_deletion, inframe_insertion, "
  84                     + "missense_variant, stop_lost]");
  85
  86     /*
  87      * coding_sequence_variant further adds synonymous_variant
  88      */
  89     terms = map.get("coding_sequence_variant");
  90     assertEquals(terms.size(), 6);
  91     assertEquals(terms.toString(),
  92             "[frameshift_variant, inframe_deletion, inframe_insertion, "
  93                     + "missense_variant, stop_lost, synonymous_variant]");
  94
  95     /*
  96      * coding_transcript_variant further adds 5_prime_UTR_variant
  97      */
  98     terms = map.get("coding_transcript_variant");
  99     assertEquals(terms.size(), 7);
 100     assertEquals(terms.toString(),
 101             "[5_prime_UTR_variant, frameshift_variant, inframe_deletion, "
 102                     + "inframe_insertion, missense_variant, stop_lost, synonymous_variant]");
 103
 104     /*
 105      * exon_variant further adds non_coding_transcript_exon_variant
 106      */
 107     terms = map.get("exon_variant");
 108     assertEquals(terms.size(), 8);
 109     assertEquals(terms.toString(),
 110             "[5_prime_UTR_variant, frameshift_variant, inframe_deletion, "
 111                     + "inframe_insertion, missense_variant, "
 112                     + "non_coding_transcript_exon_variant, stop_lost, synonymous_variant]");
 113
 114     /*
 115      * transcript_variant further adds splice_region_variant
 116      */
 117     terms = map.get("transcript_variant");
 118     assertEquals(terms.size(), 9);
 119     assertEquals(terms.toString(),
 120             "[5_prime_UTR_variant, frameshift_variant, inframe_deletion, "
 121                     + "inframe_insertion, missense_variant, "
 122                     + "non_coding_transcript_exon_variant, splice_region_variant, "
 123                     + "stop_lost, synonymous_variant]");
 124
 125     /*
 126      * feature_variant further adds upstream_gene_variant
 127      */
 128     terms = map.get("feature_variant");
 129     assertEquals(terms.size(), 10);
 130     assertEquals(terms.toString(),
 131             "[5_prime_UTR_variant, frameshift_variant, inframe_deletion, "
 132                     + "inframe_insertion, missense_variant, "
 133                     + "non_coding_transcript_exon_variant, splice_region_variant, "
 134                     + "stop_lost, synonymous_variant, upstream_gene_variant]");
 135
 136     /*
 137      * sequence_variant adds itself
 138      */
 139     terms = map.get("sequence_variant");
 140     assertEquals(terms.size(), 11);
 141     assertEquals(terms.toString(),
 142             "[5_prime_UTR_variant, frameshift_variant, inframe_deletion, "
 143                     + "inframe_insertion, missense_variant, "
 144                     + "non_coding_transcript_exon_variant, sequence_variant, splice_region_variant, "
 145                     + "stop_lost, synonymous_variant, upstream_gene_variant]");
 146   }
 147
 148 }