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