test/jalview/ext/ensembl/EnsemblCdsTest.java

   1 /*
   2  * Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
   3  * Copyright (C) $$Year-Rel$$ The Jalview Authors
   4  *
   5  * This file is part of Jalview.
   6  *
   7  * Jalview is free software: you can redistribute it and/or
   8  * modify it under the terms of the GNU General Public License
   9  * as published by the Free Software Foundation, either version 3
  10  * of the License, or (at your option) any later version.
  11  *
  12  * Jalview is distributed in the hope that it will be useful, but
  13  * WITHOUT ANY WARRANTY; without even the implied warranty
  14  * of MERCHANTABILITY or FITNESS FOR A PARTICULAR
  15  * PURPOSE.  See the GNU General Public License for more details.
  16  *
  17  * You should have received a copy of the GNU General Public License
  18  * along with Jalview.  If not, see <http://www.gnu.org/licenses/>.
  19  * The Jalview Authors are detailed in the 'AUTHORS' file.
  20  */
  21 package jalview.ext.ensembl;
  22
  23 import static org.testng.AssertJUnit.assertEquals;
  24 import static org.testng.AssertJUnit.assertFalse;
  25 import static org.testng.AssertJUnit.assertTrue;
  26
  27 import jalview.datamodel.Sequence;
  28 import jalview.datamodel.SequenceDummy;
  29 import jalview.datamodel.SequenceFeature;
  30 import jalview.datamodel.SequenceI;
  31 import jalview.gui.JvOptionPane;
  32 import jalview.io.gff.SequenceOntologyFactory;
  33 import jalview.io.gff.SequenceOntologyLite;
  34 import jalview.util.MapList;
  35
  36 import java.util.List;
  37
  38 import org.testng.Assert;
  39 import org.testng.annotations.AfterClass;
  40 import org.testng.annotations.BeforeClass;
  41 import org.testng.annotations.Test;
  42
  43 public class EnsemblCdsTest
  44 {
  45
  46   @BeforeClass(alwaysRun = true)
  47   public void setUpJvOptionPane()
  48   {
  49     JvOptionPane.setInteractiveMode(false);
  50     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  51   }
  52
  53   @BeforeClass(alwaysRun = true)
  54   public void setUp()
  55   {
  56     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
  57   }
  58
  59   @AfterClass(alwaysRun = true)
  60   public void tearDown()
  61   {
  62     SequenceOntologyFactory.setInstance(null);
  63   }
  64
  65   /**
  66    * Test that the cdna part of genomic sequence is correctly identified by
  67    * 'CDS' features (or subtypes) with the desired transcript as parent
  68    */
  69   @Test(groups = "Functional")
  70   public void testGetGenomicRangesFromFeatures()
  71   {
  72     EnsemblCds testee = new EnsemblCds();
  73     SequenceI genomic = new SequenceDummy("chr7");
  74     genomic.setStart(10000);
  75     genomic.setEnd(50000);
  76     String transcriptId = "ABC123";
  77
  78     // CDS at (start+10000) length 501
  79     SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
  80             null);
  81     sf.setValue("Parent", "transcript:" + transcriptId);
  82     sf.setStrand("+");
  83     genomic.addSequenceFeature(sf);
  84
  85     // CDS (sub-type) at (start + 10500) length 101
  86     sf = new SequenceFeature("CDS_predicted", "", 10500, 10600, 0f, null);
  87     sf.setValue("Parent", "transcript:" + transcriptId);
  88     sf.setStrand("+");
  89     genomic.addSequenceFeature(sf);
  90
  91     // CDS belonging to a different transcript doesn't count
  92     sf = new SequenceFeature("CDS", "", 11500, 12600, 0f, null);
  93     sf.setValue("Parent", "transcript:anotherOne");
  94     genomic.addSequenceFeature(sf);
  95
  96     // exon feature doesn't count
  97     sf = new SequenceFeature("exon", "", 10000, 50000, 0f, null);
  98     genomic.addSequenceFeature(sf);
  99
 100     // mRNA_region feature doesn't count (parent of CDS)
 101     sf = new SequenceFeature("mRNA_region", "", 10000, 50000, 0f, null);
 102     genomic.addSequenceFeature(sf);
 103
 104     MapList ranges = testee.getGenomicRangesFromFeatures(genomic,
 105             transcriptId, 23);
 106     List<int[]> fromRanges = ranges.getFromRanges();
 107     assertEquals(2, fromRanges.size());
 108     // from ranges should be sorted by start order
 109     assertEquals(10500, fromRanges.get(0)[0]);
 110     assertEquals(10600, fromRanges.get(0)[1]);
 111     assertEquals(20000, fromRanges.get(1)[0]);
 112     assertEquals(20500, fromRanges.get(1)[1]);
 113     // to range should start from given start numbering
 114     List<int[]> toRanges = ranges.getToRanges();
 115     assertEquals(1, toRanges.size());
 116     assertEquals(23, toRanges.get(0)[0]);
 117     assertEquals(624, toRanges.get(0)[1]);
 118   }
 119
 120   /**
 121    * Test the method that retains features except for 'CDS' (or subtypes), or
 122    * features with parent other than the given id
 123    */
 124   @Test(groups = "Functional")
 125   public void testRetainFeature()
 126   {
 127     String accId = "ABC123";
 128     EnsemblCds testee = new EnsemblCds();
 129
 130     SequenceFeature sf = new SequenceFeature("CDS", "", 20000, 20500, 0f,
 131             null);
 132     assertFalse(testee.retainFeature(sf, accId));
 133
 134     sf = new SequenceFeature("CDS_predicted", "", 20000, 20500, 0f, null);
 135     assertFalse(testee.retainFeature(sf, accId));
 136
 137     // other feature with no parent is retained
 138     sf = new SequenceFeature("CDS_psequence_variantredicted", "", 20000,
 139             20500, 0f, null);
 140     assertTrue(testee.retainFeature(sf, accId));
 141
 142     // other feature with desired parent is retained
 143     sf.setValue("Parent", "transcript:" + accId);
 144     assertTrue(testee.retainFeature(sf, accId));
 145
 146     // feature with wrong parent is not retained
 147     sf.setValue("Parent", "transcript:XYZ");
 148     assertFalse(testee.retainFeature(sf, accId));
 149   }
 150
 151   /**
 152    * Test the method that picks out 'CDS' (or subtype) features with the
 153    * accession id as parent
 154    */
 155   @Test(groups = "Functional")
 156   public void testGetIdentifyingFeatures()
 157   {
 158     String accId = "ABC123";
 159     SequenceI seq = new Sequence(accId, "MKDONS");
 160
 161     // cds with no parent not valid
 162     SequenceFeature sf1 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
 163     seq.addSequenceFeature(sf1);
 164
 165     // cds with wrong parent not valid
 166     SequenceFeature sf2 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
 167     sf2.setValue("Parent", "transcript:XYZ");
 168     seq.addSequenceFeature(sf2);
 169
 170     // cds with right parent is valid
 171     SequenceFeature sf3 = new SequenceFeature("CDS", "", 1, 2, 0f, null);
 172     sf3.setValue("Parent", "transcript:" + accId);
 173     seq.addSequenceFeature(sf3);
 174
 175     // cds sub-type with right parent is valid
 176     SequenceFeature sf4 = new SequenceFeature("CDS_predicted", "", 1, 2, 0f,
 177             null);
 178     sf4.setValue("Parent", "transcript:" + accId);
 179     seq.addSequenceFeature(sf4);
 180
 181     // transcript not valid:
 182     SequenceFeature sf5 = new SequenceFeature("transcript", "", 1, 2, 0f,
 183             null);
 184     sf5.setValue("Parent", "transcript:" + accId);
 185     seq.addSequenceFeature(sf5);
 186
 187     // exon not valid:
 188     SequenceFeature sf6 = new SequenceFeature("exon", "", 1, 2, 0f, null);
 189     sf6.setValue("Parent", "transcript:" + accId);
 190     seq.addSequenceFeature(sf6);
 191
 192     List<SequenceFeature> sfs = new EnsemblCds().getIdentifyingFeatures(seq,
 193             accId);
 194     assertFalse(sfs.contains(sf1));
 195     assertFalse(sfs.contains(sf2));
 196     assertTrue(sfs.contains(sf3));
 197     assertTrue(sfs.contains(sf4));
 198     assertFalse(sfs.contains(sf5));
 199     assertFalse(sfs.contains(sf6));
 200   }
 201
 202   @Test(groups = "Functional")
 203   public void testIsValidReference() throws Exception
 204   {
 205     EnsemblSequenceFetcher esq = new EnsemblCds();
 206     Assert.assertTrue(esq.isValidReference("CCDS5863.1"));
 207     Assert.assertTrue(esq.isValidReference("ENST00000288602"));
 208     Assert.assertTrue(esq.isValidReference("ENSG00000288602"));
 209     Assert.assertTrue(esq.isValidReference("ENSP00000288602"));
 210     Assert.assertFalse(esq.isValidReference("ENST0000288602"));
 211     // non-human species have a 3 character identifier included:
 212     Assert.assertTrue(esq.isValidReference("ENSMUSG00000099398"));
 213   }
 214
 215 }