test/jalview/ext/ensembl/EnsemblCdsTest.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.Assert;
  17 import org.testng.annotations.AfterClass;
  18 import org.testng.annotations.BeforeClass;
  19 import org.testng.annotations.Test;
  20
  21 public class EnsemblCdsTest
  22 {
  23   @BeforeClass(alwaysRun = true)
  24   public void setUp()
  25   {
  26     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
  27   }
  28
  29   @AfterClass(alwaysRun = true)
  30   public void tearDown()
  31   {
  32     SequenceOntologyFactory.setInstance(null);
  33   }
  34
  35   /**
  36    * Test that the cdna part of genomic sequence is correctly identified by
  37    * 'CDS' features (or subtypes) with the desired transcript as parent
  38    */
  39   @Test(groups = "Functional")
  40   public void testGetGenomicRangesFromFeatures()
  41   {
  42     EnsemblCds testee = new EnsemblCds();
  43     SequenceI genomic = new SequenceDummy("chr7");
  44     genomic.setStart(10000);
  45     genomic.setEnd(50000);
  46     String transcriptId = "ABC123";
  47
  48     // CDS at (start+10000) length 501
  49     SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
  50             null);
  51     sf.setValue("Parent", "transcript:" + transcriptId);
  52     sf.setStrand("+");
  53     genomic.addSequenceFeature(sf);
  54
  55     // CDS (sub-type) at (start + 10500) length 101
  56     sf = new SequenceFeature("CDS_predicted", "", 10500, 10600, 0f, null);
  57     sf.setValue("Parent", "transcript:" + transcriptId);
  58     sf.setStrand("+");
  59     genomic.addSequenceFeature(sf);
  60
  61     // CDS belonging to a different transcript doesn't count
  62     sf = new SequenceFeature("CDS", "", 11500, 12600, 0f, null);
  63     sf.setValue("Parent", "transcript:anotherOne");
  64     genomic.addSequenceFeature(sf);
  65
  66     // exon feature doesn't count
  67     sf = new SequenceFeature("exon", "", 10000, 50000, 0f, null);
  68     genomic.addSequenceFeature(sf);
  69
  70     // mRNA_region feature doesn't count (parent of CDS)
  71     sf = new SequenceFeature("mRNA_region", "", 10000, 50000, 0f, null);
  72     genomic.addSequenceFeature(sf);
  73
  74     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
  75             transcriptId, 23);
  76     List<int[]> fromRanges = ranges.getFromRanges();
  77     assertEquals(2, fromRanges.size());
  78     // from ranges should be sorted by start order
  79     assertEquals(10500, fromRanges.get(0)[0]);
  80     assertEquals(10600, fromRanges.get(0)[1]);
  81     assertEquals(20000, fromRanges.get(1)[0]);
  82     assertEquals(20500, fromRanges.get(1)[1]);
  83     // to range should start from given start numbering
  84     List<int[]> toRanges = ranges.getToRanges();
  85     assertEquals(1, toRanges.size());
  86     assertEquals(23, toRanges.get(0)[0]);
  87     assertEquals(624, toRanges.get(0)[1]);
  88   }
  89
  90   /**
  91    * Test the method that retains features except for 'CDS' (or subtypes), or
  92    * features with parent other than the given id
  93    */
  94   @Test(groups = "Functional")
  95   public void testRetainFeature()
  96   {
  97     String accId = "ABC123";
  98     EnsemblCds testee = new EnsemblCds();
  99
 100     SequenceFeature sf = new SequenceFeature("CDS", "", 20000,
 101             20500, 0f, null);
 102     assertFalse(testee.retainFeature(sf, accId));
 103
 104     sf.setType("CDS_predicted");
 105     assertFalse(testee.retainFeature(sf, accId));
 106
 107     // other feature with no parent is retained
 108     sf.setType("sequence_variant");
 109     assertTrue(testee.retainFeature(sf, accId));
 110
 111     // other feature with desired parent is retained
 112     sf.setValue("Parent", "transcript:" + accId);
 113     assertTrue(testee.retainFeature(sf, accId));
 114
 115     // feature with wrong parent is not retained
 116     sf.setValue("Parent", "transcript:XYZ");
 117     assertFalse(testee.retainFeature(sf, accId));
 118   }
 119
 120   /**
 121    * Test the method that picks out 'CDS' (or subtype) features with the
 122    * accession id as parent
 123    */
 124   @Test(groups = "Functional")
 125   public void testIdentifiesSequence()
 126   {
 127     String accId = "ABC123";
 128     EnsemblCds testee = new EnsemblCds();
 129
 130     // cds with no parent not valid
 131     SequenceFeature sf = new SequenceFeature("CDS", "", 1, 2, 0f, null);
 132     assertFalse(testee.identifiesSequence(sf, accId));
 133
 134     // cds with wrong parent not valid
 135     sf.setValue("Parent", "transcript:XYZ");
 136     assertFalse(testee.identifiesSequence(sf, accId));
 137
 138     // cds with right parent is valid
 139     sf.setValue("Parent", "transcript:" + accId);
 140     assertTrue(testee.identifiesSequence(sf, accId));
 141
 142     // cds sub-type with right parent is valid
 143     sf.setType("CDS_predicted");
 144     assertTrue(testee.identifiesSequence(sf, accId));
 145
 146     // transcript not valid:
 147     sf.setType("transcript");
 148     assertFalse(testee.identifiesSequence(sf, accId));
 149
 150     // exon not valid:
 151     sf.setType("exon");
 152     assertFalse(testee.identifiesSequence(sf, accId));
 153   }
 154
 155   @Test(groups = "Functional")
 156   public void testIsValidReference() throws Exception
 157   {
 158     EnsemblSequenceFetcher esq = new EnsemblCds();
 159     Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
 160     Assert.assertTrue(esq.isValidReference("ENST00000288602"));
 161     Assert.assertTrue(esq.isValidReference("ENSG00000288602"));
 162     Assert.assertTrue(esq.isValidReference("ENSP00000288602"));
 163     Assert.assertFalse(esq.isValidReference("ENST0000288602"));
 164     // non-human species have a 3 character identifier included:
 165     Assert.assertTrue(esq.isValidReference("ENSMUSG00000099398"));
 166   }
 167
 168 }