test/jalview/ext/ensembl/EnsemblCdnaTest.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.assertNull;
   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.Assert;
  18 import org.testng.annotations.AfterClass;
  19 import org.testng.annotations.BeforeClass;
  20 import org.testng.annotations.Test;
  21
  22 public class EnsemblCdnaTest
  23 {
  24   @BeforeClass(alwaysRun = true)
  25   public void setUp()
  26   {
  27     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
  28   }
  29
  30   @AfterClass(alwaysRun = true)
  31   public void tearDown()
  32   {
  33     SequenceOntologyFactory.setInstance(null);
  34   }
  35
  36   /**
  37    * Test that the cdna part of genomic sequence is correctly identified by
  38    * 'exon' features (or subtypes) - reverse strand case.
  39    */
  40   @Test(groups = "Functional")
  41   public void testGetGenomicRangesFromFeatures_reverseStrand()
  42   {
  43     EnsemblCdna testee = new EnsemblCdna();
  44     SequenceI genomic = new SequenceDummy("chr7");
  45     genomic.setStart(10000);
  46     genomic.setEnd(50000);
  47     String transcriptId = "ABC123";
  48
  49     // exon at (start+10000) length 501
  50     SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
  51             null);
  52     sf.setValue("Parent", "transcript:" + transcriptId);
  53     sf.setStrand("-");
  54     genomic.addSequenceFeature(sf);
  55
  56     // exon (sub-type) at (start + exon_variant) length 101
  57     sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
  58     sf.setValue("Parent", "transcript:" + transcriptId);
  59     sf.setStrand("-");
  60     genomic.addSequenceFeature(sf);
  61
  62     // exon belonging to a different transcript doesn't count
  63     sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
  64     sf.setValue("Parent", "transcript:anotherOne");
  65     genomic.addSequenceFeature(sf);
  66
  67     // transcript feature doesn't count
  68     sf = new SequenceFeature("transcript", "", 10000, 50000, 0f, null);
  69     genomic.addSequenceFeature(sf);
  70
  71     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
  72             transcriptId, 23);
  73     List<int[]> fromRanges = ranges.getFromRanges();
  74     assertEquals(2, fromRanges.size());
  75
  76     /*
  77      * from ranges should be sorted by start order descending
  78      * and hold mappings from reverse strand sense
  79      */
  80     assertEquals(20500, fromRanges.get(0)[0]);
  81     assertEquals(20000, fromRanges.get(0)[1]);
  82     assertEquals(10600, fromRanges.get(1)[0]);
  83     assertEquals(10500, fromRanges.get(1)[1]);
  84     // to range should start from given start numbering
  85     List<int[]> toRanges = ranges.getToRanges();
  86     assertEquals(1, toRanges.size());
  87     assertEquals(23, toRanges.get(0)[0]);
  88     assertEquals(624, toRanges.get(0)[1]);
  89   }
  90
  91   /**
  92    * Test that the cdna part of genomic sequence is correctly identified by
  93    * 'exon' features (or subtypes) with the desired transcript as parent
  94    */
  95   @Test(groups = "Functional")
  96   public void testGetGenomicRangesFromFeatures()
  97   {
  98     EnsemblCdna testee = new EnsemblCdna();
  99     SequenceI genomic = new SequenceDummy("chr7");
 100     genomic.setStart(10000);
 101     genomic.setEnd(50000);
 102     String transcriptId = "ABC123";
 103
 104     // exon at (start+10000) length 501
 105     SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
 106             null);
 107     sf.setValue("Parent", "transcript:" + transcriptId);
 108     sf.setStrand("+");
 109     genomic.addSequenceFeature(sf);
 110
 111     // exon (sub-type) at (start + exon_variant) length 101
 112     sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
 113     sf.setValue("Parent", "transcript:" + transcriptId);
 114     sf.setStrand("+");
 115     genomic.addSequenceFeature(sf);
 116
 117     // exon belonging to a different transcript doesn't count
 118     sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
 119     sf.setValue("Parent", "transcript:anotherOne");
 120     genomic.addSequenceFeature(sf);
 121
 122     // transcript feature doesn't count
 123     sf = new SequenceFeature("transcript", "", 10000, 50000, 0f, null);
 124     sf.setStrand("-"); // weird but ignored
 125     genomic.addSequenceFeature(sf);
 126
 127     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
 128             transcriptId, 23);
 129     List<int[]> fromRanges = ranges.getFromRanges();
 130     assertEquals(2, fromRanges.size());
 131     // from ranges should be sorted by start order
 132     assertEquals(10500, fromRanges.get(0)[0]);
 133     assertEquals(10600, fromRanges.get(0)[1]);
 134     assertEquals(20000, fromRanges.get(1)[0]);
 135     assertEquals(20500, fromRanges.get(1)[1]);
 136     // to range should start from given start numbering
 137     List<int[]> toRanges = ranges.getToRanges();
 138     assertEquals(1, toRanges.size());
 139     assertEquals(23, toRanges.get(0)[0]);
 140     assertEquals(624, toRanges.get(0)[1]);
 141   }
 142
 143   /**
 144    * The method under test should give up and return null if both forward and
 145    * reverse strands are present in the features of interest
 146    */
 147   @Test(groups = "Functional")
 148   public void testGetGenomicRangesFromFeatures_mixedStrand()
 149   {
 150     EnsemblCdna testee = new EnsemblCdna();
 151     SequenceI genomic = new SequenceDummy("chr7");
 152     genomic.setStart(10000);
 153     genomic.setEnd(50000);
 154     String transcriptId = "ABC123";
 155
 156     SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
 157             null);
 158     sf.setValue("Parent", "transcript:" + transcriptId);
 159     sf.setStrand("-");
 160     genomic.addSequenceFeature(sf);
 161
 162     sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
 163     sf.setValue("Parent", "transcript:" + transcriptId);
 164     sf.setStrand("+");
 165     genomic.addSequenceFeature(sf);
 166
 167     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
 168             transcriptId, 23);
 169     assertNull(ranges);
 170   }
 171
 172   /**
 173    * Test the method that retains features except for 'transcript' (or
 174    * subtypes), or features with parent other than the given id
 175    */
 176   @Test(groups = "Functional")
 177   public void testRetainFeature()
 178   {
 179     String accId = "ABC123";
 180     EnsemblCdna testee = new EnsemblCdna();
 181
 182     SequenceFeature sf = new SequenceFeature("transcript", "", 20000,
 183             20500, 0f, null);
 184     assertFalse(testee.retainFeature(sf, accId));
 185
 186     sf.setType("aberrant_processed_transcript");
 187     assertFalse(testee.retainFeature(sf, accId));
 188
 189     sf.setType("NMD_transcript_variant");
 190     assertFalse(testee.retainFeature(sf, accId));
 191
 192     // other feature with no parent is retained
 193     sf.setType("sequence_variant");
 194     assertTrue(testee.retainFeature(sf, accId));
 195
 196     // other feature with desired parent is retained
 197     sf.setValue("Parent", "transcript:" + accId);
 198     assertTrue(testee.retainFeature(sf, accId));
 199
 200     // feature with wrong parent is not retained
 201     sf.setValue("Parent", "transcript:XYZ");
 202     assertFalse(testee.retainFeature(sf, accId));
 203   }
 204
 205   /**
 206    * Test the method that picks out 'exon' (or subtype) features with the
 207    * accession id as parent
 208    */
 209   @Test(groups = "Functional")
 210   public void testIdentifiesSequence()
 211   {
 212     String accId = "ABC123";
 213     EnsemblCdna testee = new EnsemblCdna();
 214
 215     // exon with no parent not valid
 216     SequenceFeature sf = new SequenceFeature("exon", "", 1, 2, 0f, null);
 217     assertFalse(testee.identifiesSequence(sf, accId));
 218
 219     // exon with wrong parent not valid
 220     sf.setValue("Parent", "transcript:XYZ");
 221     assertFalse(testee.identifiesSequence(sf, accId));
 222
 223     // exon with right parent is valid
 224     sf.setValue("Parent", "transcript:" + accId);
 225     assertTrue(testee.identifiesSequence(sf, accId));
 226
 227     // exon sub-type with right parent is valid
 228     sf.setType("coding_exon");
 229     assertTrue(testee.identifiesSequence(sf, accId));
 230
 231     // transcript not valid:
 232     sf.setType("transcript");
 233     assertFalse(testee.identifiesSequence(sf, accId));
 234
 235     // CDS not valid:
 236     sf.setType("CDS");
 237     assertFalse(testee.identifiesSequence(sf, accId));
 238   }
 239
 240   @Test(groups = "Functional")
 241   public void testIsValidReference() throws Exception
 242   {
 243     EnsemblSequenceFetcher esq = new EnsemblCdna();
 244     Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
 245     Assert.assertTrue(esq.isValidReference("ENST00000288602"));
 246     Assert.assertTrue(esq.isValidReference("ENSG00000288602"));
 247     Assert.assertFalse(esq.isValidReference("ENSP00000288602"));
 248     Assert.assertFalse(esq.isValidReference("ENST0000288602"));
 249     // non-human species having a 3 character identifier included:
 250     Assert.assertTrue(esq.isValidReference("ENSMUSG00000099398"));
 251   }
 252 }