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.gui.JvOptionPane;
  32 import jalview.io.DataSourceType;
  33 import jalview.io.FastaFile;
  34 import jalview.io.FileParse;
  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
  41 import org.testng.Assert;
  42 import org.testng.annotations.AfterClass;
  43 import org.testng.annotations.BeforeClass;
  44 import org.testng.annotations.DataProvider;
  45 import org.testng.annotations.Test;
  46
  47 public class EnsemblSeqProxyTest
  48 {
  49
  50   @BeforeClass(alwaysRun = true)
  51   public void setUpJvOptionPane()
  52   {
  53     JvOptionPane.setInteractiveMode(false);
  54     JvOptionPane.setMockResponse(JvOptionPane.CANCEL_OPTION);
  55   }
  56
  57   private static final Object[][] allSeqs = new Object[][] {
  58       {
  59           new EnsemblProtein(),
  60           "CCDS5863.1",
  61           ">CCDS5863.1\n"
  62                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  63                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
  64                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
  65                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
  66                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
  67                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
  68                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
  69                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
  70                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
  71                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
  72                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
  73                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
  74                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
  75       {
  76           new EnsemblCdna(),
  77           "CCDS5863.1",
  78           ">CCDS5863.1\n"
  79                   + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
  80                   + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
  81                   + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
  82                   + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
  83                   + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
  84                   + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
  85                   + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
  86                   + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
  87                   + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
  88                   + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
  89                   + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
  90                   + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
  91                   + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
  92                   + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
  93                   + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
  94                   + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
  95                   + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
  96                   + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
  97                   + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
  98                   + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
  99                   + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
 100                   + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
 101                   + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
 102                   + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
 103                   + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
 104                   + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
 105                   + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
 106                   + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
 107                   + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
 108                   + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
 109                   + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
 110                   + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
 111                   + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
 112                   + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
 113                   + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
 114                   + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
 115                   + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
 116                   + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
 117                   + "GGTGCGTTTCCTGTCCACTGA\n" },
 118       {
 119           new EnsemblProtein(),
 120           "ENSP00000288602",
 121           ">ENSP00000288602\n"
 122                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
 123                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
 124                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
 125                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
 126                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
 127                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
 128                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
 129                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
 130                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
 131                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
 132                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
 133                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
 134                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
 135
 136   @BeforeClass(alwaysRun = true)
 137   public void setUp()
 138   {
 139     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
 140   }
 141
 142   @AfterClass(alwaysRun = true)
 143   public void tearDown()
 144   {
 145     SequenceOntologyFactory.setInstance(null);
 146   }
 147
 148   @DataProvider(name = "ens_seqs")
 149   public Object[][] createData(Method m)
 150   {
 151     System.out.println(m.getName());
 152     return allSeqs;
 153   }
 154
 155   @Test(dataProvider = "ens_seqs", suiteName = "live")
 156   public void testGetOneSeqs(EnsemblRestClient proxy, String sq,
 157           String fastasq) throws Exception
 158   {
 159     FileParse fp = proxy.getSequenceReader(Arrays
 160             .asList(new String[] { sq }));
 161     SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
 162     FastaFile trueRes = new FastaFile(fastasq, DataSourceType.PASTE);
 163     SequenceI[] trueSqs = trueRes.getSeqsAsArray();
 164     Assert.assertEquals(sqs.length, trueSqs.length,
 165             "Different number of sequences retrieved for query " + sq);
 166     Alignment ral = new Alignment(sqs);
 167     for (SequenceI tr : trueSqs)
 168     {
 169       SequenceI[] rseq;
 170       Assert.assertNotNull(
 171               rseq = ral.findSequenceMatch(tr.getName()),
 172               "Couldn't find sequences matching expected sequence "
 173                       + tr.getName());
 174       Assert.assertEquals(rseq.length, 1,
 175               "Expected only one sequence for sequence ID " + tr.getName());
 176       Assert.assertEquals(
 177               rseq[0].getSequenceAsString(),
 178               tr.getSequenceAsString(),
 179               "Sequences differ for " + tr.getName() + "\n" + "Exp:"
 180                       + tr.getSequenceAsString() + "\n" + "Got:"
 181                       + rseq[0].getSequenceAsString());
 182
 183     }
 184   }
 185
 186   @Test(groups = "Functional")
 187   public void getGenomicRangesFromFeatures()
 188   {
 189
 190   }
 191
 192   @Test(groups = "Functional")
 193   public void testIsTranscriptIdentifier()
 194   {
 195     EnsemblSeqProxy testee = new EnsemblGene();
 196     assertFalse(testee.isTranscriptIdentifier(null));
 197     assertFalse(testee.isTranscriptIdentifier(""));
 198     assertFalse(testee.isTranscriptIdentifier("ENSG00000012345"));
 199     assertTrue(testee.isTranscriptIdentifier("ENST00000012345"));
 200     assertTrue(testee.isTranscriptIdentifier("ENSMUST00000012345"));
 201     assertFalse(testee.isTranscriptIdentifier("enst00000012345"));
 202     assertFalse(testee.isTranscriptIdentifier("ENST000000123456"));
 203     assertFalse(testee.isTranscriptIdentifier("ENST0000001234"));
 204   }
 205
 206   @Test(groups = "Functional")
 207   public void testIsGeneIdentifier()
 208   {
 209     EnsemblSeqProxy testee = new EnsemblGene();
 210     assertFalse(testee.isGeneIdentifier(null));
 211     assertFalse(testee.isGeneIdentifier(""));
 212     assertFalse(testee.isGeneIdentifier("ENST00000012345"));
 213     assertTrue(testee.isGeneIdentifier("ENSG00000012345"));
 214     assertTrue(testee.isGeneIdentifier("ENSMUSG00000012345"));
 215     assertFalse(testee.isGeneIdentifier("ensg00000012345"));
 216     assertFalse(testee.isGeneIdentifier("ENSG000000123456"));
 217     assertFalse(testee.isGeneIdentifier("ENSG0000001234"));
 218   }
 219
 220   /**
 221    * Test the method that appends a single allele's reverse complement to a
 222    * string buffer
 223    */
 224   @Test(groups = "Functional")
 225   public void testReverseComplementAllele()
 226   {
 227     StringBuilder sb = new StringBuilder();
 228     EnsemblSeqProxy.reverseComplementAllele(sb, "G"); // comp=C
 229     EnsemblSeqProxy.reverseComplementAllele(sb, "g"); // comp=c
 230     EnsemblSeqProxy.reverseComplementAllele(sb, "C"); // comp=G
 231     EnsemblSeqProxy.reverseComplementAllele(sb, "T"); // comp=A
 232     EnsemblSeqProxy.reverseComplementAllele(sb, "A"); // comp=T
 233     assertEquals("C,c,G,A,T", sb.toString());
 234
 235     sb = new StringBuilder();
 236     EnsemblSeqProxy.reverseComplementAllele(sb, "-GATt"); // revcomp=aATC-
 237     EnsemblSeqProxy.reverseComplementAllele(sb, "hgmd_mutation");
 238     EnsemblSeqProxy.reverseComplementAllele(sb, "PhenCode_variation");
 239     assertEquals("aATC-,hgmd_mutation,PhenCode_variation", sb.toString());
 240   }
 241
 242   /**
 243    * Test the method that computes the reverse complement of the alleles in a
 244    * sequence_variant feature
 245    */
 246   @Test(groups = "Functional")
 247   public void testReverseComplementAlleles()
 248   {
 249     String alleles = "C,G,-TAC,HGMD_MUTATION,gac";
 250     SequenceFeature sf = new SequenceFeature("sequence_variant", alleles,
 251             1, 2, 0f, null);
 252     sf.setValue("alleles", alleles);
 253     sf.setAttributes("x=y,z;alleles=" + alleles + ";a=b,c");
 254
 255     EnsemblSeqProxy.reverseComplementAlleles(sf);
 256     String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc";
 257     // verify description is updated with reverse complement
 258     assertEquals(revcomp, sf.getDescription());
 259     // verify alleles attribute is updated with reverse complement
 260     assertEquals(revcomp, sf.getValue("alleles"));
 261     // verify attributes string is updated with reverse complement
 262     assertEquals("x=y,z;alleles=" + revcomp + ";a=b,c", sf.getAttributes());
 263   }
 264
 265   @Test(groups = "Functional")
 266   public void testSortFeatures()
 267   {
 268     SequenceFeature sf1 = new SequenceFeature("", "", 10, 15, 0f, null);
 269     SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
 270     SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
 271     SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
 272     SequenceFeature[] sfs = new SequenceFeature[] { sf1, sf2, sf3, sf4 };
 273
 274     // sort by start position ascending (forward strand)
 275     // sf2 and sf3 tie and should not be reordered by sorting
 276     EnsemblSeqProxy.sortFeatures(sfs, true);
 277     assertArrayEquals(new SequenceFeature[] { sf2, sf3, sf1, sf4 }, sfs);
 278
 279     // sort by end position descending (reverse strand)
 280     EnsemblSeqProxy.sortFeatures(sfs, false);
 281     assertArrayEquals(new SequenceFeature[] { sf1, sf3, sf2, sf4 }, sfs);
 282   }
 283 }