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       {
  54           new EnsemblProtein(),
  55           "CCDS5863.1",
  56           ">CCDS5863.1\n"
  57                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  58                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
  59                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
  60                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
  61                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
  62                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
  63                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
  64                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
  65                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
  66                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
  67                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
  68                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
  69                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
  70       {
  71           new EnsemblCdna(),
  72           "CCDS5863.1",
  73           ">CCDS5863.1\n"
  74                   + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
  75                   + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
  76                   + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
  77                   + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
  78                   + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
  79                   + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
  80                   + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
  81                   + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
  82                   + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
  83                   + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
  84                   + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
  85                   + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
  86                   + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
  87                   + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
  88                   + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
  89                   + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
  90                   + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
  91                   + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
  92                   + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
  93                   + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
  94                   + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
  95                   + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
  96                   + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
  97                   + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
  98                   + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
  99                   + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
 100                   + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
 101                   + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
 102                   + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
 103                   + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
 104                   + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
 105                   + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
 106                   + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
 107                   + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
 108                   + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
 109                   + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
 110                   + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
 111                   + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
 112                   + "GGTGCGTTTCCTGTCCACTGA\n" },
 113       {
 114           new EnsemblProtein(),
 115           "ENSP00000288602",
 116           ">ENSP00000288602\n"
 117                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
 118                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
 119                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
 120                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
 121                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
 122                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
 123                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDG\n"
 124                   // ? insertion added in ENSP00000288602.11, not in P15056
 125                   + "APLNQLMRCLRKYQSRTPSPLLHSVPSEIVFDFEPGPVFR\n"
 126                   // end insertion
 127                   + "GSTTGLSATPPASLPGSLTNVKALQKSP\n"
 128                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
 129                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
 130                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
 131                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
 132                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
 133                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
 134
 135   @BeforeClass(alwaysRun = true)
 136   public void setUp()
 137   {
 138     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
 139   }
 140
 141   @AfterClass(alwaysRun = true)
 142   public void tearDown()
 143   {
 144     SequenceOntologyFactory.setInstance(null);
 145   }
 146
 147   @DataProvider(name = "ens_seqs")
 148   public Object[][] createData(Method m)
 149   {
 150     System.out.println(m.getName());
 151     return allSeqs;
 152   }
 153
 154   @Test(dataProvider = "ens_seqs", suiteName = "live")
 155   public void testGetSequenceRecords(EnsemblSeqProxy proxy, String sq,
 156           String fastasq) throws Exception
 157   {
 158     FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE);
 159     SequenceI[] expected = trueRes.getSeqsAsArray();
 160     AlignmentI retrieved = proxy.getSequenceRecords(sq);
 161
 162     Assert.assertEquals(retrieved.getHeight(), expected.length,
 163             "Different number of sequences retrieved for query " + sq);
 164
 165     for (SequenceI tr : expected)
 166     {
 167       SequenceI[] rseq;
 168       Assert.assertNotNull(
 169               rseq = retrieved.findSequenceMatch(tr.getName()),
 170               "Couldn't find sequences matching expected sequence "
 171                       + tr.getName());
 172       Assert.assertEquals(rseq.length, 1,
 173               "Expected only one sequence for sequence ID " + tr.getName());
 174       Assert.assertEquals(
 175               rseq[0].getSequenceAsString(),
 176               tr.getSequenceAsString(),
 177               "Sequences differ for " + tr.getName() + "\n" + "Exp:"
 178                       + tr.getSequenceAsString() + "\n" + "Got:"
 179                       + rseq[0].getSequenceAsString());
 180     }
 181   }
 182
 183   @Test(groups = "Functional")
 184   public void getGenomicRangesFromFeatures()
 185   {
 186
 187   }
 188
 189   /**
 190    * Test the method that appends a single allele's reverse complement to a
 191    * string buffer
 192    */
 193   @Test(groups = "Functional")
 194   public void testReverseComplementAllele()
 195   {
 196     StringBuilder sb = new StringBuilder();
 197     EnsemblSeqProxy.reverseComplementAllele(sb, "G"); // comp=C
 198     EnsemblSeqProxy.reverseComplementAllele(sb, "g"); // comp=c
 199     EnsemblSeqProxy.reverseComplementAllele(sb, "C"); // comp=G
 200     EnsemblSeqProxy.reverseComplementAllele(sb, "T"); // comp=A
 201     EnsemblSeqProxy.reverseComplementAllele(sb, "A"); // comp=T
 202     assertEquals("C,c,G,A,T", sb.toString());
 203
 204     sb = new StringBuilder();
 205     EnsemblSeqProxy.reverseComplementAllele(sb, "-GATt"); // revcomp=aATC-
 206     EnsemblSeqProxy.reverseComplementAllele(sb, "hgmd_mutation");
 207     EnsemblSeqProxy.reverseComplementAllele(sb, "PhenCode_variation");
 208     assertEquals("aATC-,hgmd_mutation,PhenCode_variation", sb.toString());
 209   }
 210
 211   /**
 212    * Test the method that computes the reverse complement of the alleles in a
 213    * sequence_variant feature
 214    */
 215   @Test(groups = "Functional")
 216   public void testReverseComplementAlleles()
 217   {
 218     String alleles = "C,G,-TAC,HGMD_MUTATION,gac";
 219     SequenceFeature sf = new SequenceFeature("sequence_variant", alleles,
 220             1, 2, 0f, null);
 221     sf.setValue("alleles", alleles);
 222
 223     EnsemblSeqProxy.reverseComplementAlleles(sf);
 224     String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc";
 225     // verify description is updated with reverse complement
 226     assertEquals(revcomp, sf.getDescription());
 227     // verify alleles attribute is updated with reverse complement
 228     assertEquals(revcomp, sf.getValue("alleles"));
 229   }
 230 }