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_nucleotide()
  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      * hierarchy from stop_gained
  46      */
  47     Map<String, List<String>> map = SequenceOntologyFactory.getInstance()
  48             .findSequenceOntologyGroupings("stop_gained", featureTypes);
  49     assertEquals(map.size(), 10);
  50
  51     /*
  52      * feature_truncation adds inframe_deletion
  53      */
  54     List<String> terms = map.get("feature_truncation");
  55     assertEquals(terms.size(), 1);
  56     assertTrue(terms.contains("inframe_deletion"));
  57
  58     /*
  59      * nonsynonymous_variant adds stop_lost, missense_variant
  60      */
  61     terms = map.get("nonsynonymous_variant");
  62     assertEquals(terms.size(), 2);
  63     assertEquals(terms.toString(), "[missense_variant, stop_lost]");
  64
  65     /*
  66      * inframe_variant further adds inframe_deletion, inframe_insertion
  67      */
  68     terms = map.get("inframe_variant");
  69     assertEquals(terms.size(), 4);
  70     assertEquals(terms.toString(),
  71             "[inframe_deletion, inframe_insertion, missense_variant, stop_lost]");
  72
  73     /*
  74      * protein_altering_variant further adds frameshift_variant
  75      */
  76     terms = map.get("protein_altering_variant");
  77     assertEquals(terms.size(), 5);
  78     assertEquals(terms.toString(),
  79             "[frameshift_variant, inframe_deletion, inframe_insertion, "
  80                     + "missense_variant, stop_lost]");
  81
  82     /*
  83      * coding_sequence_variant further adds synonymous_variant
  84      */
  85     terms = map.get("coding_sequence_variant");
  86     assertEquals(terms.size(), 6);
  87     assertEquals(terms.toString(),
  88             "[frameshift_variant, inframe_deletion, inframe_insertion, "
  89                     + "missense_variant, stop_lost, synonymous_variant]");
  90
  91     /*
  92      * coding_transcript_variant further adds 5_prime_UTR_variant
  93      */
  94     terms = map.get("coding_transcript_variant");
  95     assertEquals(terms.size(), 7);
  96     assertEquals(terms.toString(),
  97             "[5_prime_UTR_variant, frameshift_variant, inframe_deletion, "
  98                     + "inframe_insertion, missense_variant, stop_lost, synonymous_variant]");
  99
 100     /*
 101      * exon_variant further adds non_coding_transcript_exon_variant
 102      */
 103     terms = map.get("exon_variant");
 104     assertEquals(terms.size(), 8);
 105     assertEquals(terms.toString(),
 106             "[5_prime_UTR_variant, frameshift_variant, inframe_deletion, "
 107                     + "inframe_insertion, missense_variant, "
 108                     + "non_coding_transcript_exon_variant, stop_lost, synonymous_variant]");
 109
 110     /*
 111      * transcript_variant further adds splice_region_variant
 112      */
 113     terms = map.get("transcript_variant");
 114     assertEquals(terms.size(), 9);
 115     assertEquals(terms.toString(),
 116             "[5_prime_UTR_variant, frameshift_variant, inframe_deletion, "
 117                     + "inframe_insertion, missense_variant, "
 118                     + "non_coding_transcript_exon_variant, splice_region_variant, "
 119                     + "stop_lost, synonymous_variant]");
 120
 121     /*
 122      * feature_variant further adds upstream_gene_variant
 123      */
 124     terms = map.get("feature_variant");
 125     assertEquals(terms.size(), 10);
 126     assertEquals(terms.toString(),
 127             "[5_prime_UTR_variant, frameshift_variant, inframe_deletion, "
 128                     + "inframe_insertion, missense_variant, "
 129                     + "non_coding_transcript_exon_variant, splice_region_variant, "
 130                     + "stop_lost, synonymous_variant, upstream_gene_variant]");
 131
 132     /*
 133      * sequence_variant adds itself
 134      */
 135     terms = map.get("sequence_variant");
 136     assertEquals(terms.size(), 11);
 137     assertEquals(terms.toString(),
 138             "[5_prime_UTR_variant, frameshift_variant, inframe_deletion, "
 139                     + "inframe_insertion, missense_variant, "
 140                     + "non_coding_transcript_exon_variant, sequence_variant, splice_region_variant, "
 141                     + "stop_lost, synonymous_variant, upstream_gene_variant]");
 142   }
 143
 144   @Test(groups = "Functional")
 145   public void testfindSequenceOntologyGroupings_peptide()
 146   {
 147     /*
 148      * typical Uniprot feature types
 149      */
 150     List<String> featureTypes = Arrays.asList("BETA-TURN-IR", "NEST-RL",
 151             "BETA-BULGE", "ALPHA-BETA-MOTIF", "ASX-TURN-IR",
 152             "GAMMA-TURN-CLASSIC", "GAMMA-TURN-INVERSE", "BETA-TURN-IL",
 153             "BETA-TURN-IIL");
 154
 155     /*
 156      * hierarchy from GAMMA-TURN-INVERSE
 157      * this is a synonym for
 158      */
 159     Map<String, List<String>> map = SequenceOntologyFactory.getInstance()
 160             .findSequenceOntologyGroupings("TURN", featureTypes);
 161     assertEquals(map.size(), 10);
 162   }
 163
 164 }