test/jalview/ext/ensembl/EnsemblSeqProxyTest.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.assertSame;
  26 import static org.testng.AssertJUnit.assertTrue;
  27
  28 import jalview.datamodel.Alignment;
  29 import jalview.datamodel.SequenceFeature;
  30 import jalview.datamodel.SequenceI;
  31 import jalview.datamodel.features.SequenceFeatures;
  32 import jalview.gui.JvOptionPane;
  33 import jalview.io.DataSourceType;
  34 import jalview.io.FastaFile;
  35 import jalview.io.FileParse;
  36 import jalview.io.gff.SequenceOntologyFactory;
  37 import jalview.io.gff.SequenceOntologyLite;
  38
  39 import java.lang.reflect.Method;
  40 import java.util.Arrays;
  41 import java.util.List;
  42
  43 import org.testng.Assert;
  44 import org.testng.annotations.AfterClass;
  45 import org.testng.annotations.BeforeClass;
  46 import org.testng.annotations.DataProvider;
  47 import org.testng.annotations.Test;
  48
  49 public class EnsemblSeqProxyTest
  50 {
  51
  52   @BeforeClass(alwaysRun = true)
  53   public void setUpJvOptionPane()
  54   {
  55     JvOptionPane.setInteractiveMode(false);
  56     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  57   }
  58
  59   private static final Object[][] allSeqs = new Object[][] {
  60       {
  61           new EnsemblProtein(),
  62           "CCDS5863.1",
  63           ">CCDS5863.1\n"
  64                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  65                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
  66                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
  67                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
  68                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
  69                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
  70                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
  71                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
  72                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
  73                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
  74                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
  75                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
  76                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
  77       {
  78           new EnsemblCdna(),
  79           "CCDS5863.1",
  80           ">CCDS5863.1\n"
  81                   + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
  82                   + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
  83                   + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
  84                   + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
  85                   + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
  86                   + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
  87                   + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
  88                   + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
  89                   + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
  90                   + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
  91                   + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
  92                   + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
  93                   + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
  94                   + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
  95                   + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
  96                   + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
  97                   + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
  98                   + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
  99                   + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
 100                   + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
 101                   + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
 102                   + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
 103                   + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
 104                   + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
 105                   + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
 106                   + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
 107                   + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
 108                   + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
 109                   + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
 110                   + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
 111                   + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
 112                   + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
 113                   + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
 114                   + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
 115                   + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
 116                   + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
 117                   + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
 118                   + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
 119                   + "GGTGCGTTTCCTGTCCACTGA\n" },
 120       {
 121           new EnsemblProtein(),
 122           "ENSP00000288602",
 123           ">ENSP00000288602\n"
 124                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
 125                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
 126                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
 127                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
 128                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
 129                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
 130                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
 131                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
 132                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
 133                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
 134                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
 135                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
 136                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
 137
 138   @BeforeClass(alwaysRun = true)
 139   public void setUp()
 140   {
 141     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
 142   }
 143
 144   @AfterClass(alwaysRun = true)
 145   public void tearDown()
 146   {
 147     SequenceOntologyFactory.setInstance(null);
 148   }
 149
 150   @DataProvider(name = "ens_seqs")
 151   public Object[][] createData(Method m)
 152   {
 153     System.out.println(m.getName());
 154     return allSeqs;
 155   }
 156
 157   @Test(dataProvider = "ens_seqs", suiteName = "live")
 158   public void testGetOneSeqs(EnsemblRestClient proxy, String sq,
 159           String fastasq) throws Exception
 160   {
 161     FileParse fp = proxy.getSequenceReader(Arrays
 162             .asList(new String[] { sq }));
 163     SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
 164     FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE);
 165     SequenceI[] trueSqs = trueRes.getSeqsAsArray();
 166     Assert.assertEquals(sqs.length, trueSqs.length,
 167             "Different number of sequences retrieved for query " + sq);
 168     Alignment ral = new Alignment(sqs);
 169     for (SequenceI tr : trueSqs)
 170     {
 171       // 12/05/2017 failing for EnsemblCdna which is returning protein
 172       // Ensembl helpdesk ticket 187998
 173       SequenceI[] rseq;
 174       Assert.assertNotNull(
 175               rseq = ral.findSequenceMatch(tr.getName()),
 176               "Couldn't find sequences matching expected sequence "
 177                       + tr.getName());
 178       Assert.assertEquals(rseq.length, 1,
 179               "Expected only one sequence for sequence ID " + tr.getName());
 180       Assert.assertEquals(
 181               rseq[0].getSequenceAsString(),
 182               tr.getSequenceAsString(),
 183               "Sequences differ for " + tr.getName() + "\n" + "Exp:"
 184                       + tr.getSequenceAsString() + "\n" + "Got:"
 185                       + rseq[0].getSequenceAsString());
 186
 187     }
 188   }
 189
 190   @Test(groups = "Functional")
 191   public void getGenomicRangesFromFeatures()
 192   {
 193
 194   }
 195
 196   @Test(groups = "Functional")
 197   public void testIsTranscriptIdentifier()
 198   {
 199     EnsemblSeqProxy testee = new EnsemblGene();
 200     assertFalse(testee.isTranscriptIdentifier(null));
 201     assertFalse(testee.isTranscriptIdentifier(""));
 202     assertFalse(testee.isTranscriptIdentifier("ENSG00000012345"));
 203     assertTrue(testee.isTranscriptIdentifier("ENST00000012345"));
 204     assertTrue(testee.isTranscriptIdentifier("ENSMUST00000012345"));
 205     assertFalse(testee.isTranscriptIdentifier("enst00000012345"));
 206     assertFalse(testee.isTranscriptIdentifier("ENST000000123456"));
 207     assertFalse(testee.isTranscriptIdentifier("ENST0000001234"));
 208   }
 209
 210   @Test(groups = "Functional")
 211   public void testIsGeneIdentifier()
 212   {
 213     EnsemblSeqProxy testee = new EnsemblGene();
 214     assertFalse(testee.isGeneIdentifier(null));
 215     assertFalse(testee.isGeneIdentifier(""));
 216     assertFalse(testee.isGeneIdentifier("ENST00000012345"));
 217     assertTrue(testee.isGeneIdentifier("ENSG00000012345"));
 218     assertTrue(testee.isGeneIdentifier("ENSMUSG00000012345"));
 219     assertFalse(testee.isGeneIdentifier("ensg00000012345"));
 220     assertFalse(testee.isGeneIdentifier("ENSG000000123456"));
 221     assertFalse(testee.isGeneIdentifier("ENSG0000001234"));
 222   }
 223
 224   /**
 225    * Test the method that appends a single allele's reverse complement to a
 226    * string buffer
 227    */
 228   @Test(groups = "Functional")
 229   public void testReverseComplementAllele()
 230   {
 231     StringBuilder sb = new StringBuilder();
 232     EnsemblSeqProxy.reverseComplementAllele(sb, "G"); // comp=C
 233     EnsemblSeqProxy.reverseComplementAllele(sb, "g"); // comp=c
 234     EnsemblSeqProxy.reverseComplementAllele(sb, "C"); // comp=G
 235     EnsemblSeqProxy.reverseComplementAllele(sb, "T"); // comp=A
 236     EnsemblSeqProxy.reverseComplementAllele(sb, "A"); // comp=T
 237     assertEquals("C,c,G,A,T", sb.toString());
 238
 239     sb = new StringBuilder();
 240     EnsemblSeqProxy.reverseComplementAllele(sb, "-GATt"); // revcomp=aATC-
 241     EnsemblSeqProxy.reverseComplementAllele(sb, "hgmd_mutation");
 242     EnsemblSeqProxy.reverseComplementAllele(sb, "PhenCode_variation");
 243     assertEquals("aATC-,hgmd_mutation,PhenCode_variation", sb.toString());
 244   }
 245
 246   /**
 247    * Test the method that computes the reverse complement of the alleles in a
 248    * sequence_variant feature
 249    */
 250   @Test(groups = "Functional")
 251   public void testReverseComplementAlleles()
 252   {
 253     String alleles = "C,G,-TAC,HGMD_MUTATION,gac";
 254     SequenceFeature sf = new SequenceFeature("sequence_variant", alleles,
 255             1, 2, 0f, null);
 256     sf.setValue("alleles", alleles);
 257     sf.setAttributes("x=y,z;alleles=" + alleles + ";a=b,c");
 258
 259     EnsemblSeqProxy.reverseComplementAlleles(sf);
 260     String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc";
 261     // verify description is updated with reverse complement
 262     assertEquals(revcomp, sf.getDescription());
 263     // verify alleles attribute is updated with reverse complement
 264     assertEquals(revcomp, sf.getValue("alleles"));
 265     // verify attributes string is updated with reverse complement
 266     assertEquals("x=y,z;alleles=" + revcomp + ";a=b,c", sf.getAttributes());
 267   }
 268
 269   @Test(groups = "Functional")
 270   public void testSortFeatures()
 271   {
 272     SequenceFeature sf1 = new SequenceFeature("", "", 10, 15, 0f, null);
 273     SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
 274     SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
 275     SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
 276     List<SequenceFeature> sfs = Arrays.asList(new SequenceFeature[] { sf1,
 277         sf2, sf3, sf4 });
 278
 279     // sort by start position ascending (forward strand)
 280     // sf2 and sf3 tie and should not be reordered by sorting
 281     SequenceFeatures.sortFeatures(sfs, true);
 282     assertSame(sfs.get(0), sf2);
 283     assertSame(sfs.get(1), sf3);
 284     assertSame(sfs.get(2), sf1);
 285     assertSame(sfs.get(3), sf4);
 286
 287     // sort by end position descending (reverse strand)
 288     SequenceFeatures.sortFeatures(sfs, false);
 289     assertSame(sfs.get(0), sf1);
 290     assertSame(sfs.get(1), sf3);
 291     assertSame(sfs.get(2), sf2);
 292     assertSame(sfs.get(3), sf4);
 293   }
 294 }