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.AlignmentI;
  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.gff.SequenceOntologyFactory;
  36 import jalview.io.gff.SequenceOntologyLite;
  37
  38 import java.lang.reflect.Method;
  39 import java.util.Arrays;
  40 import java.util.List;
  41
  42 import org.testng.Assert;
  43 import org.testng.annotations.AfterClass;
  44 import org.testng.annotations.BeforeClass;
  45 import org.testng.annotations.DataProvider;
  46 import org.testng.annotations.Test;
  47
  48 public class EnsemblSeqProxyTest
  49 {
  50
  51   @BeforeClass(alwaysRun = true)
  52   public void setUpJvOptionPane()
  53   {
  54     JvOptionPane.setInteractiveMode(false);
  55     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  56   }
  57
  58   private static final Object[][] allSeqs = new Object[][] {
  59       {
  60           new EnsemblProtein(),
  61           "CCDS5863.1",
  62           ">CCDS5863.1\n"
  63                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  64                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
  65                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
  66                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
  67                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
  68                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
  69                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
  70                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
  71                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
  72                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
  73                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
  74                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
  75                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
  76       {
  77           new EnsemblCdna(),
  78           "CCDS5863.1",
  79           ">CCDS5863.1\n"
  80                   + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
  81                   + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
  82                   + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
  83                   + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
  84                   + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
  85                   + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
  86                   + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
  87                   + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
  88                   + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
  89                   + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
  90                   + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
  91                   + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
  92                   + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
  93                   + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
  94                   + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
  95                   + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
  96                   + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
  97                   + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
  98                   + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
  99                   + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
 100                   + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
 101                   + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
 102                   + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
 103                   + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
 104                   + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
 105                   + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
 106                   + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
 107                   + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
 108                   + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
 109                   + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
 110                   + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
 111                   + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
 112                   + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
 113                   + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
 114                   + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
 115                   + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
 116                   + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
 117                   + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
 118                   + "GGTGCGTTTCCTGTCCACTGA\n" },
 119       {
 120           new EnsemblProtein(),
 121           "ENSP00000288602",
 122           ">ENSP00000288602\n"
 123                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
 124                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
 125                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
 126                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
 127                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
 128                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
 129                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDG\n"
 130                   // ? insertion added in ENSP00000288602.11, not in P15056
 131                   + "APLNQLMRCLRKYQSRTPSPLLHSVPSEIVFDFEPGPVFR\n"
 132                   // end insertion
 133                   + "GSTTGLSATPPASLPGSLTNVKALQKSP\n"
 134                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
 135                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
 136                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
 137                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
 138                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
 139                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
 140
 141   @BeforeClass(alwaysRun = true)
 142   public void setUp()
 143   {
 144     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
 145   }
 146
 147   @AfterClass(alwaysRun = true)
 148   public void tearDown()
 149   {
 150     SequenceOntologyFactory.setInstance(null);
 151   }
 152
 153   @DataProvider(name = "ens_seqs")
 154   public Object[][] createData(Method m)
 155   {
 156     System.out.println(m.getName());
 157     return allSeqs;
 158   }
 159
 160   @Test(dataProvider = "ens_seqs", suiteName = "live")
 161   public void testGetSequenceRecords(EnsemblSeqProxy proxy, String sq,
 162           String fastasq) throws Exception
 163   {
 164     FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE);
 165     SequenceI[] expected = trueRes.getSeqsAsArray();
 166     AlignmentI retrieved = proxy.getSequenceRecords(sq);
 167
 168     Assert.assertEquals(retrieved.getHeight(), expected.length,
 169             "Different number of sequences retrieved for query " + sq);
 170
 171     for (SequenceI tr : expected)
 172     {
 173       SequenceI[] rseq;
 174       Assert.assertNotNull(
 175               rseq = retrieved.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   @Test(groups = "Functional")
 190   public void getGenomicRangesFromFeatures()
 191   {
 192
 193   }
 194
 195   /**
 196    * Test the method that appends a single allele's reverse complement to a
 197    * string buffer
 198    */
 199   @Test(groups = "Functional")
 200   public void testReverseComplementAllele()
 201   {
 202     StringBuilder sb = new StringBuilder();
 203     EnsemblSeqProxy.reverseComplementAllele(sb, "G"); // comp=C
 204     EnsemblSeqProxy.reverseComplementAllele(sb, "g"); // comp=c
 205     EnsemblSeqProxy.reverseComplementAllele(sb, "C"); // comp=G
 206     EnsemblSeqProxy.reverseComplementAllele(sb, "T"); // comp=A
 207     EnsemblSeqProxy.reverseComplementAllele(sb, "A"); // comp=T
 208     assertEquals("C,c,G,A,T", sb.toString());
 209
 210     sb = new StringBuilder();
 211     EnsemblSeqProxy.reverseComplementAllele(sb, "-GATt"); // revcomp=aATC-
 212     EnsemblSeqProxy.reverseComplementAllele(sb, "hgmd_mutation");
 213     EnsemblSeqProxy.reverseComplementAllele(sb, "PhenCode_variation");
 214     assertEquals("aATC-,hgmd_mutation,PhenCode_variation", sb.toString());
 215   }
 216
 217   /**
 218    * Test the method that computes the reverse complement of the alleles in a
 219    * sequence_variant feature
 220    */
 221   @Test(groups = "Functional")
 222   public void testReverseComplementAlleles()
 223   {
 224     String alleles = "C,G,-TAC,HGMD_MUTATION,gac";
 225     SequenceFeature sf = new SequenceFeature("sequence_variant", alleles,
 226             1, 2, 0f, null);
 227     sf.setValue("alleles", alleles);
 228     sf.setAttributes("x=y,z;alleles=" + alleles + ";a=b,c");
 229
 230     EnsemblSeqProxy.reverseComplementAlleles(sf);
 231     String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc";
 232     // verify description is updated with reverse complement
 233     assertEquals(revcomp, sf.getDescription());
 234     // verify alleles attribute is updated with reverse complement
 235     assertEquals(revcomp, sf.getValue("alleles"));
 236     // verify attributes string is updated with reverse complement
 237     assertEquals("x=y,z;alleles=" + revcomp + ";a=b,c", sf.getAttributes());
 238   }
 239
 240   @Test(groups = "Functional")
 241   public void testSortFeatures()
 242   {
 243     SequenceFeature sf1 = new SequenceFeature("", "", 10, 15, 0f, null);
 244     SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
 245     SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
 246     SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
 247     List<SequenceFeature> sfs = Arrays.asList(new SequenceFeature[] { sf1,
 248         sf2, sf3, sf4 });
 249
 250     // sort by start position ascending (forward strand)
 251     // sf2 and sf3 tie and should not be reordered by sorting
 252     SequenceFeatures.sortFeatures(sfs, true);
 253     assertSame(sfs.get(0), sf2);
 254     assertSame(sfs.get(1), sf3);
 255     assertSame(sfs.get(2), sf1);
 256     assertSame(sfs.get(3), sf4);
 257
 258     // sort by end position descending (reverse strand)
 259     SequenceFeatures.sortFeatures(sfs, false);
 260     assertSame(sfs.get(0), sf1);
 261     assertSame(sfs.get(1), sf3);
 262     assertSame(sfs.get(2), sf2);
 263     assertSame(sfs.get(3), sf4);
 264   }
 265 }