test/jalview/ext/ensembl/EnsemblSeqProxyTest.java

   1 package jalview.ext.ensembl;
   2
   3 import static org.testng.AssertJUnit.assertEquals;
   4 import static org.testng.AssertJUnit.assertFalse;
   5 import static org.testng.AssertJUnit.assertTrue;
   6 import static org.testng.internal.junit.ArrayAsserts.assertArrayEquals;
   7
   8 import jalview.datamodel.Alignment;
   9 import jalview.datamodel.SequenceFeature;
  10 import jalview.datamodel.SequenceI;
  11 import jalview.io.AppletFormatAdapter;
  12 import jalview.io.FastaFile;
  13 import jalview.io.FileParse;
  14 import jalview.io.gff.SequenceOntologyFactory;
  15 import jalview.io.gff.SequenceOntologyLite;
  16
  17 import java.lang.reflect.Method;
  18 import java.util.Arrays;
  19
  20 import org.testng.Assert;
  21 import org.testng.annotations.AfterClass;
  22 import org.testng.annotations.BeforeClass;
  23 import org.testng.annotations.DataProvider;
  24 import org.testng.annotations.Test;
  25
  26
  27 public class EnsemblSeqProxyTest
  28 {
  29   private static final Object[][] allSeqs = new Object[][] {
  30       {
  31           new EnsemblProtein(),
  32           "CCDS5863.1",
  33           ">CCDS5863.1\n"
  34                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  35                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
  36                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
  37                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
  38                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
  39                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
  40                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
  41                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
  42                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
  43                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
  44                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
  45                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
  46                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
  47       {
  48           new EnsemblCdna(),
  49           "CCDS5863.1",
  50           ">CCDS5863.1\n"
  51                   + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
  52                   + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
  53                   + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
  54                   + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
  55                   + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
  56                   + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
  57                   + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
  58                   + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
  59                   + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
  60                   + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
  61                   + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
  62                   + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
  63                   + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
  64                   + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
  65                   + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
  66                   + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
  67                   + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
  68                   + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
  69                   + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
  70                   + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
  71                   + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
  72                   + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
  73                   + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
  74                   + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
  75                   + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
  76                   + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
  77                   + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
  78                   + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
  79                   + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
  80                   + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
  81                   + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
  82                   + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
  83                   + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
  84                   + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
  85                   + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
  86                   + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
  87                   + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
  88                   + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
  89                   + "GGTGCGTTTCCTGTCCACTGA\n" },
  90       {
  91           new EnsemblProtein(),
  92           "ENSP00000288602",
  93           ">ENSP00000288602\n"
  94                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  95                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
  96                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
  97                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
  98                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
  99                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
 100                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
 101                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
 102                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
 103                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
 104                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
 105                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
 106                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
 107
 108   @BeforeClass(alwaysRun = true)
 109   public void setUp()
 110   {
 111     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
 112   }
 113
 114   @AfterClass(alwaysRun = true)
 115   public void tearDown()
 116   {
 117     SequenceOntologyFactory.setInstance(null);
 118   }
 119
 120   @DataProvider(name = "ens_seqs")
 121   public Object[][] createData(Method m)
 122   {
 123     System.out.println(m.getName());
 124     return allSeqs;
 125   }
 126
 127   @Test(dataProvider = "ens_seqs", suiteName = "live")
 128   public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq)
 129           throws Exception
 130   {
 131     FileParse fp = proxy.getSequenceReader(Arrays
 132             .asList(new String[]
 133     { sq }));
 134     SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
 135     FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
 136     SequenceI[] trueSqs = trueRes.getSeqsAsArray();
 137     Assert.assertEquals(sqs.length, trueSqs.length,
 138             "Different number of sequences retrieved for query " + sq);
 139     Alignment ral = new Alignment(sqs);
 140     for (SequenceI tr : trueSqs)
 141     {
 142       SequenceI[] rseq;
 143       Assert.assertNotNull(
 144               rseq = ral.findSequenceMatch(tr.getName()),
 145               "Couldn't find sequences matching expected sequence "
 146                       + tr.getName());
 147       Assert.assertEquals(rseq.length, 1,
 148               "Expected only one sequence for sequence ID " + tr.getName());
 149       Assert.assertEquals(
 150               rseq[0].getSequenceAsString(),
 151               tr.getSequenceAsString(),
 152               "Sequences differ for " + tr.getName() + "\n" + "Exp:"
 153                       + tr.getSequenceAsString() + "\n" + "Got:"
 154                       + rseq[0].getSequenceAsString());
 155
 156     }
 157   }
 158
 159   @Test(groups = "Functional")
 160   public void getGenomicRangesFromFeatures()
 161   {
 162
 163   }
 164
 165   @Test(groups = "Functional")
 166   public void testIsTranscriptIdentifier()
 167   {
 168     EnsemblSeqProxy testee = new EnsemblGene();
 169     assertFalse(testee.isTranscriptIdentifier(null));
 170     assertFalse(testee.isTranscriptIdentifier(""));
 171     assertFalse(testee.isTranscriptIdentifier("ENSG00000012345"));
 172     assertTrue(testee.isTranscriptIdentifier("ENST00000012345"));
 173     assertTrue(testee.isTranscriptIdentifier("ENSMUST00000012345"));
 174     assertFalse(testee.isTranscriptIdentifier("enst00000012345"));
 175     assertFalse(testee.isTranscriptIdentifier("ENST000000123456"));
 176     assertFalse(testee.isTranscriptIdentifier("ENST0000001234"));
 177   }
 178
 179   @Test(groups = "Functional")
 180   public void testIsGeneIdentifier()
 181   {
 182     EnsemblSeqProxy testee = new EnsemblGene();
 183     assertFalse(testee.isGeneIdentifier(null));
 184     assertFalse(testee.isGeneIdentifier(""));
 185     assertFalse(testee.isGeneIdentifier("ENST00000012345"));
 186     assertTrue(testee.isGeneIdentifier("ENSG00000012345"));
 187     assertTrue(testee.isGeneIdentifier("ENSMUSG00000012345"));
 188     assertFalse(testee.isGeneIdentifier("ensg00000012345"));
 189     assertFalse(testee.isGeneIdentifier("ENSG000000123456"));
 190     assertFalse(testee.isGeneIdentifier("ENSG0000001234"));
 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     SequenceFeature[] sfs = new SequenceFeature[] { sf1, sf2, sf3, sf4 };
 246
 247     // sort by start position ascending (forward strand)
 248     // sf2 and sf3 tie and should not be reordered by sorting
 249     EnsemblSeqProxy.sortFeatures(sfs, true);
 250     assertArrayEquals(new SequenceFeature[] { sf2, sf3, sf1, sf4 }, sfs);
 251
 252     // sort by end position descending (reverse strand)
 253     EnsemblSeqProxy.sortFeatures(sfs, false);
 254     assertArrayEquals(new SequenceFeature[] { sf1, sf3, sf2, sf4 }, sfs);
 255   }
 256 }