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.assertSame;
  25
  26 import jalview.datamodel.AlignmentI;
  27 import jalview.datamodel.SequenceFeature;
  28 import jalview.datamodel.SequenceI;
  29 import jalview.datamodel.features.SequenceFeatures;
  30 import jalview.gui.JvOptionPane;
  31 import jalview.io.DataSourceType;
  32 import jalview.io.FastaFile;
  33 import jalview.io.gff.SequenceOntologyFactory;
  34 import jalview.io.gff.SequenceOntologyLite;
  35
  36 import java.lang.reflect.Method;
  37 import java.util.Arrays;
  38 import java.util.List;
  39
  40 import org.testng.Assert;
  41 import org.testng.annotations.AfterClass;
  42 import org.testng.annotations.BeforeClass;
  43 import org.testng.annotations.DataProvider;
  44 import org.testng.annotations.Test;
  45
  46 public class EnsemblSeqProxyTest
  47 {
  48
  49   @BeforeClass(alwaysRun = true)
  50   public void setUpJvOptionPane()
  51   {
  52     JvOptionPane.setInteractiveMode(false);
  53     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  54   }
  55
  56   private static final Object[][] allSeqs = new Object[][] {
  57       {
  58           new EnsemblProtein(),
  59           "CCDS5863.1",
  60           ">CCDS5863.1\n"
  61                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  62                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
  63                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
  64                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
  65                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
  66                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
  67                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
  68                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
  69                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
  70                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
  71                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
  72                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
  73                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
  74       {
  75           new EnsemblCdna(),
  76           "CCDS5863.1",
  77           ">CCDS5863.1\n"
  78                   + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
  79                   + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
  80                   + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
  81                   + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
  82                   + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
  83                   + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
  84                   + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
  85                   + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
  86                   + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
  87                   + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
  88                   + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
  89                   + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
  90                   + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
  91                   + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
  92                   + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
  93                   + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
  94                   + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
  95                   + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
  96                   + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
  97                   + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
  98                   + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
  99                   + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
 100                   + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
 101                   + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
 102                   + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
 103                   + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
 104                   + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
 105                   + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
 106                   + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
 107                   + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
 108                   + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
 109                   + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
 110                   + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
 111                   + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
 112                   + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
 113                   + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
 114                   + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
 115                   + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
 116                   + "GGTGCGTTTCCTGTCCACTGA\n" },
 117       {
 118           new EnsemblProtein(),
 119           "ENSP00000288602",
 120           ">ENSP00000288602\n"
 121                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
 122                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
 123                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
 124                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
 125                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
 126                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
 127                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDG\n"
 128                   // ? insertion added in ENSP00000288602.11, not in P15056
 129                   + "APLNQLMRCLRKYQSRTPSPLLHSVPSEIVFDFEPGPVFR\n"
 130                   // end insertion
 131                   + "GSTTGLSATPPASLPGSLTNVKALQKSP\n"
 132                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
 133                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
 134                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
 135                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
 136                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
 137                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
 138
 139   @BeforeClass(alwaysRun = true)
 140   public void setUp()
 141   {
 142     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
 143   }
 144
 145   @AfterClass(alwaysRun = true)
 146   public void tearDown()
 147   {
 148     SequenceOntologyFactory.setInstance(null);
 149   }
 150
 151   @DataProvider(name = "ens_seqs")
 152   public Object[][] createData(Method m)
 153   {
 154     System.out.println(m.getName());
 155     return allSeqs;
 156   }
 157
 158   @Test(dataProvider = "ens_seqs", suiteName = "live")
 159   public void testGetSequenceRecords(EnsemblSeqProxy proxy, String sq,
 160           String fastasq) throws Exception
 161   {
 162     FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE);
 163     SequenceI[] expected = trueRes.getSeqsAsArray();
 164     AlignmentI retrieved = proxy.getSequenceRecords(sq);
 165
 166     Assert.assertEquals(retrieved.getHeight(), expected.length,
 167             "Different number of sequences retrieved for query " + sq);
 168
 169     for (SequenceI tr : expected)
 170     {
 171       SequenceI[] rseq;
 172       Assert.assertNotNull(
 173               rseq = retrieved.findSequenceMatch(tr.getName()),
 174               "Couldn't find sequences matching expected sequence "
 175                       + tr.getName());
 176       Assert.assertEquals(rseq.length, 1,
 177               "Expected only one sequence for sequence ID " + tr.getName());
 178       Assert.assertEquals(
 179               rseq[0].getSequenceAsString(),
 180               tr.getSequenceAsString(),
 181               "Sequences differ for " + tr.getName() + "\n" + "Exp:"
 182                       + tr.getSequenceAsString() + "\n" + "Got:"
 183                       + rseq[0].getSequenceAsString());
 184     }
 185   }
 186
 187   @Test(groups = "Functional")
 188   public void getGenomicRangesFromFeatures()
 189   {
 190
 191   }
 192
 193   /**
 194    * Test the method that appends a single allele's reverse complement to a
 195    * string buffer
 196    */
 197   @Test(groups = "Functional")
 198   public void testReverseComplementAllele()
 199   {
 200     StringBuilder sb = new StringBuilder();
 201     EnsemblSeqProxy.reverseComplementAllele(sb, "G"); // comp=C
 202     EnsemblSeqProxy.reverseComplementAllele(sb, "g"); // comp=c
 203     EnsemblSeqProxy.reverseComplementAllele(sb, "C"); // comp=G
 204     EnsemblSeqProxy.reverseComplementAllele(sb, "T"); // comp=A
 205     EnsemblSeqProxy.reverseComplementAllele(sb, "A"); // comp=T
 206     assertEquals("C,c,G,A,T", sb.toString());
 207
 208     sb = new StringBuilder();
 209     EnsemblSeqProxy.reverseComplementAllele(sb, "-GATt"); // revcomp=aATC-
 210     EnsemblSeqProxy.reverseComplementAllele(sb, "hgmd_mutation");
 211     EnsemblSeqProxy.reverseComplementAllele(sb, "PhenCode_variation");
 212     assertEquals("aATC-,hgmd_mutation,PhenCode_variation", sb.toString());
 213   }
 214
 215   /**
 216    * Test the method that computes the reverse complement of the alleles in a
 217    * sequence_variant feature
 218    */
 219   @Test(groups = "Functional")
 220   public void testReverseComplementAlleles()
 221   {
 222     String alleles = "C,G,-TAC,HGMD_MUTATION,gac";
 223     SequenceFeature sf = new SequenceFeature("sequence_variant", alleles,
 224             1, 2, 0f, null);
 225     sf.setValue("alleles", alleles);
 226     sf.setAttributes("x=y,z;alleles=" + alleles + ";a=b,c");
 227
 228     EnsemblSeqProxy.reverseComplementAlleles(sf);
 229     String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc";
 230     // verify description is updated with reverse complement
 231     assertEquals(revcomp, sf.getDescription());
 232     // verify alleles attribute is updated with reverse complement
 233     assertEquals(revcomp, sf.getValue("alleles"));
 234     // verify attributes string is updated with reverse complement
 235     assertEquals("x=y,z;alleles=" + revcomp + ";a=b,c", sf.getAttributes());
 236   }
 237
 238   @Test(groups = "Functional")
 239   public void testSortFeatures()
 240   {
 241     SequenceFeature sf1 = new SequenceFeature("", "", 10, 15, 0f, null);
 242     SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
 243     SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
 244     SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
 245     List<SequenceFeature> sfs = Arrays.asList(new SequenceFeature[] { sf1,
 246         sf2, sf3, sf4 });
 247
 248     // sort by start position ascending (forward strand)
 249     // sf2 and sf3 tie and should not be reordered by sorting
 250     SequenceFeatures.sortFeatures(sfs, true);
 251     assertSame(sfs.get(0), sf2);
 252     assertSame(sfs.get(1), sf3);
 253     assertSame(sfs.get(2), sf1);
 254     assertSame(sfs.get(3), sf4);
 255
 256     // sort by end position descending (reverse strand)
 257     SequenceFeatures.sortFeatures(sfs, false);
 258     assertSame(sfs.get(0), sf1);
 259     assertSame(sfs.get(1), sf3);
 260     assertSame(sfs.get(2), sf2);
 261     assertSame(sfs.get(3), sf4);
 262   }
 263 }