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.assertNull;
   5
   6 import jalview.datamodel.SequenceDummy;
   7 import jalview.datamodel.SequenceFeature;
   8 import jalview.datamodel.SequenceI;
   9 import jalview.io.gff.SequenceOntologyFactory;
  10 import jalview.io.gff.SequenceOntologyLite;
  11 import jalview.util.MapList;
  12
  13 import java.util.List;
  14
  15 import org.testng.annotations.Test;
  16
  17 public class EnsemblCdnaTest
  18 {
  19   /**
  20    * Test that the cdna part of genomic sequence is correctly identified by
  21    * 'exon' features (or subtypes) - reverse strand case.
  22    */
  23   @Test(groups = "Functional")
  24   public void getGenomicRangesFromFeatures_reverseStrand()
  25   {
  26     EnsemblCdna testee = new EnsemblCdna();
  27     SequenceI genomic = new SequenceDummy("chr7");
  28     genomic.setStart(10000);
  29     genomic.setEnd(50000);
  30     String transcriptId = "ABC123";
  31
  32     // exon at (start+10000) length 501
  33     SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
  34             null);
  35     sf.setValue("Parent", "transcript:" + transcriptId);
  36     sf.setStrand("-");
  37     genomic.addSequenceFeature(sf);
  38
  39     // exon (sub-type) at (start + exon_variant) length 101
  40     sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
  41     sf.setValue("Parent", "transcript:" + transcriptId);
  42     sf.setStrand("-");
  43     genomic.addSequenceFeature(sf);
  44
  45     // exon belonging to a different transcript doesn't count
  46     sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
  47     sf.setValue("Parent", "transcript:anotherOne");
  48     genomic.addSequenceFeature(sf);
  49
  50     // transcript feature doesn't count
  51     sf = new SequenceFeature("transcript", "", 10000, 50000, 0f, null);
  52     genomic.addSequenceFeature(sf);
  53
  54     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
  55
  56     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
  57             transcriptId, 23);
  58     List<int[]> fromRanges = ranges.getFromRanges();
  59     assertEquals(2, fromRanges.size());
  60
  61     /*
  62      * from ranges should be sorted by start order descending
  63      * and hold mappings from reverse strand sense
  64      */
  65     assertEquals(20500, fromRanges.get(0)[0]);
  66     assertEquals(20000, fromRanges.get(0)[1]);
  67     assertEquals(10600, fromRanges.get(1)[0]);
  68     assertEquals(10500, fromRanges.get(1)[1]);
  69     // to range should start from given start numbering
  70     List<int[]> toRanges = ranges.getToRanges();
  71     assertEquals(1, toRanges.size());
  72     assertEquals(23, toRanges.get(0)[0]);
  73     assertEquals(624, toRanges.get(0)[1]);
  74   }
  75
  76   /**
  77    * Test that the cdna part of genomic sequence is correctly identified by
  78    * 'exon' features (or subtypes).
  79    */
  80   @Test(groups = "Functional")
  81   public void getGenomicRangesFromFeatures()
  82   {
  83     EnsemblCdna testee = new EnsemblCdna();
  84     SequenceI genomic = new SequenceDummy("chr7");
  85     genomic.setStart(10000);
  86     genomic.setEnd(50000);
  87     String transcriptId = "ABC123";
  88
  89     // exon at (start+10000) length 501
  90     SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
  91             null);
  92     sf.setValue("Parent", "transcript:" + transcriptId);
  93     sf.setStrand("+");
  94     genomic.addSequenceFeature(sf);
  95
  96     // exon (sub-type) at (start + exon_variant) length 101
  97     sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
  98     sf.setValue("Parent", "transcript:" + transcriptId);
  99     sf.setStrand("+");
 100     genomic.addSequenceFeature(sf);
 101
 102     // exon belonging to a different transcript doesn't count
 103     sf = new SequenceFeature("exon", "", 11500, 12600, 0f, null);
 104     sf.setValue("Parent", "transcript:anotherOne");
 105     genomic.addSequenceFeature(sf);
 106
 107     // transcript feature doesn't count
 108     sf = new SequenceFeature("transcript", "", 10000, 50000, 0f, null);
 109     sf.setStrand("-"); // weird but ignored
 110     genomic.addSequenceFeature(sf);
 111
 112     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
 113
 114     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
 115             transcriptId, 23);
 116     List<int[]> fromRanges = ranges.getFromRanges();
 117     assertEquals(2, fromRanges.size());
 118     // from ranges should be sorted by start order
 119     assertEquals(10500, fromRanges.get(0)[0]);
 120     assertEquals(10600, fromRanges.get(0)[1]);
 121     assertEquals(20000, fromRanges.get(1)[0]);
 122     assertEquals(20500, fromRanges.get(1)[1]);
 123     // to range should start from given start numbering
 124     List<int[]> toRanges = ranges.getToRanges();
 125     assertEquals(1, toRanges.size());
 126     assertEquals(23, toRanges.get(0)[0]);
 127     assertEquals(624, toRanges.get(0)[1]);
 128   }
 129
 130   /**
 131    * The method under test should give up and return null if both forward and
 132    * reverse strands are present in the features of interest
 133    */
 134   @Test(groups = "Functional")
 135   public void getGenomicRangesFromFeatures_mixedStrand()
 136   {
 137     EnsemblCdna testee = new EnsemblCdna();
 138     SequenceI genomic = new SequenceDummy("chr7");
 139     genomic.setStart(10000);
 140     genomic.setEnd(50000);
 141     String transcriptId = "ABC123";
 142
 143     SequenceFeature sf = new SequenceFeature("exon", "", 20000, 20500, 0f,
 144             null);
 145     sf.setValue("Parent", "transcript:" + transcriptId);
 146     sf.setStrand("-");
 147     genomic.addSequenceFeature(sf);
 148
 149     sf = new SequenceFeature("coding_exon", "", 10500, 10600, 0f, null);
 150     sf.setValue("Parent", "transcript:" + transcriptId);
 151     sf.setStrand("+");
 152     genomic.addSequenceFeature(sf);
 153
 154     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
 155
 156     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
 157             transcriptId, 23);
 158     assertNull(ranges);
 159   }
 160 }