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
  25 import jalview.datamodel.AlignmentI;
  26 import jalview.datamodel.SequenceFeature;
  27 import jalview.datamodel.SequenceI;
  28 import jalview.gui.JvOptionPane;
  29 import jalview.io.DataSourceType;
  30 import jalview.io.FastaFile;
  31 import jalview.io.gff.SequenceOntologyFactory;
  32 import jalview.io.gff.SequenceOntologyLite;
  33
  34 import java.lang.reflect.Method;
  35
  36 import org.testng.Assert;
  37 import org.testng.annotations.AfterClass;
  38 import org.testng.annotations.BeforeClass;
  39 import org.testng.annotations.DataProvider;
  40 import org.testng.annotations.Test;
  41
  42 public class EnsemblSeqProxyTest
  43 {
  44
  45   @BeforeClass(alwaysRun = true)
  46   public void setUpJvOptionPane()
  47   {
  48     JvOptionPane.setInteractiveMode(false);
  49     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  50   }
  51
  52   private static final Object[][] allSeqs = new Object[][] { {
  53       new EnsemblProtein(), "CCDS5863.1",
  54       ">CCDS5863.1\n"
  55               + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  56               + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
  57               + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
  58               + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
  59               + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
  60               + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
  61               + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
  62               + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
  63               + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
  64               + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
  65               + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
  66               + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
  67               + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
  68       { new EnsemblCdna(), "CCDS5863.1", ">CCDS5863.1\n"
  69               + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
  70               + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
  71               + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
  72               + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
  73               + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
  74               + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
  75               + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
  76               + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
  77               + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
  78               + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
  79               + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
  80               + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
  81               + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
  82               + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
  83               + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
  84               + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
  85               + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
  86               + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
  87               + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
  88               + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
  89               + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
  90               + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
  91               + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
  92               + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
  93               + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
  94               + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
  95               + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
  96               + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
  97               + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
  98               + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
  99               + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
 100               + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
 101               + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
 102               + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
 103               + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
 104               + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
 105               + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
 106               + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
 107               + "GGTGCGTTTCCTGTCCACTGA\n" },
 108       { new EnsemblProtein(), "ENSP00000288602", ">ENSP00000288602\n"
 109               + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
 110               + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
 111               + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
 112               + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
 113               + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
 114               + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
 115               + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDG\n"
 116               // ? insertion added in ENSP00000288602.11, not in P15056
 117               + "APLNQLMRCLRKYQSRTPSPLLHSVPSEIVFDFEPGPVFR\n"
 118               // end insertion
 119               + "GSTTGLSATPPASLPGSLTNVKALQKSP\n"
 120               + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
 121               + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
 122               + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
 123               + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
 124               + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
 125               + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
 126
 127   @BeforeClass(alwaysRun = true)
 128   public void setUp()
 129   {
 130     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
 131   }
 132
 133   @AfterClass(alwaysRun = true)
 134   public void tearDown()
 135   {
 136     SequenceOntologyFactory.setInstance(null);
 137   }
 138
 139   @DataProvider(name = "ens_seqs")
 140   public Object[][] createData(Method m)
 141   {
 142     System.out.println(m.getName());
 143     return allSeqs;
 144   }
 145
 146   @Test(dataProvider = "ens_seqs", suiteName = "live")
 147   public void testGetSequenceRecords(EnsemblSeqProxy proxy, String sq,
 148           String fastasq) throws Exception
 149   {
 150     FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE);
 151     SequenceI[] expected = trueRes.getSeqsAsArray();
 152     AlignmentI retrieved = proxy.getSequenceRecords(sq);
 153
 154     Assert.assertEquals(retrieved.getHeight(), expected.length,
 155             "Different number of sequences retrieved for query " + sq);
 156
 157     for (SequenceI tr : expected)
 158     {
 159       SequenceI[] rseq;
 160       Assert.assertNotNull(rseq = retrieved.findSequenceMatch(tr.getName()),
 161               "Couldn't find sequences matching expected sequence "
 162                       + tr.getName());
 163       Assert.assertEquals(rseq.length, 1,
 164               "Expected only one sequence for sequence ID " + tr.getName());
 165       Assert.assertEquals(rseq[0].getSequenceAsString(),
 166               tr.getSequenceAsString(),
 167               "Sequences differ for " + tr.getName() + "\n" + "Exp:"
 168                       + tr.getSequenceAsString() + "\n" + "Got:"
 169                       + rseq[0].getSequenceAsString());
 170     }
 171   }
 172
 173   @Test(groups = "Functional")
 174   public void getGenomicRangesFromFeatures()
 175   {
 176
 177   }
 178
 179   /**
 180    * Test the method that appends a single allele's reverse complement to a
 181    * string buffer
 182    */
 183   @Test(groups = "Functional")
 184   public void testReverseComplementAllele()
 185   {
 186     StringBuilder sb = new StringBuilder();
 187     EnsemblSeqProxy.reverseComplementAllele(sb, "G"); // comp=C
 188     EnsemblSeqProxy.reverseComplementAllele(sb, "g"); // comp=c
 189     EnsemblSeqProxy.reverseComplementAllele(sb, "C"); // comp=G
 190     EnsemblSeqProxy.reverseComplementAllele(sb, "T"); // comp=A
 191     EnsemblSeqProxy.reverseComplementAllele(sb, "A"); // comp=T
 192     assertEquals("C,c,G,A,T", sb.toString());
 193
 194     sb = new StringBuilder();
 195     EnsemblSeqProxy.reverseComplementAllele(sb, "-GATt"); // revcomp=aATC-
 196     EnsemblSeqProxy.reverseComplementAllele(sb, "hgmd_mutation");
 197     EnsemblSeqProxy.reverseComplementAllele(sb, "PhenCode_variation");
 198     assertEquals("aATC-,hgmd_mutation,PhenCode_variation", sb.toString());
 199   }
 200
 201   /**
 202    * Test the method that computes the reverse complement of the alleles in a
 203    * sequence_variant feature
 204    */
 205   @Test(groups = "Functional")
 206   public void testReverseComplementAlleles()
 207   {
 208     String alleles = "C,G,-TAC,HGMD_MUTATION,gac";
 209     SequenceFeature sf = new SequenceFeature("sequence_variant", alleles, 1,
 210             2, 0f, null);
 211     sf.setValue("alleles", alleles);
 212
 213     EnsemblSeqProxy.reverseComplementAlleles(sf);
 214     String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc";
 215     // verify description is updated with reverse complement
 216     assertEquals(revcomp, sf.getDescription());
 217     // verify alleles attribute is updated with reverse complement
 218     assertEquals(revcomp, sf.getValue("alleles"));
 219   }
 220 }