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