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 public class EnsemblSeqProxyTest
  27 {
  28   private static final Object[][] allSeqs = new Object[][] {
  29       {
  30           new EnsemblProtein(),
  31           "CCDS5863.1",
  32           ">CCDS5863.1\n"
  33                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  34                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
  35                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
  36                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
  37                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
  38                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
  39                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
  40                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
  41                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
  42                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
  43                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
  44                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
  45                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
  46       {
  47           new EnsemblCdna(),
  48           "CCDS5863.1",
  49           ">CCDS5863.1\n"
  50                   + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
  51                   + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
  52                   + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
  53                   + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
  54                   + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
  55                   + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
  56                   + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
  57                   + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
  58                   + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
  59                   + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
  60                   + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
  61                   + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
  62                   + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
  63                   + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
  64                   + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
  65                   + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
  66                   + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
  67                   + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
  68                   + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
  69                   + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
  70                   + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
  71                   + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
  72                   + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
  73                   + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
  74                   + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
  75                   + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
  76                   + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
  77                   + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
  78                   + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
  79                   + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
  80                   + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
  81                   + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
  82                   + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
  83                   + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
  84                   + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
  85                   + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
  86                   + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
  87                   + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
  88                   + "GGTGCGTTTCCTGTCCACTGA\n" },
  89       {
  90           new EnsemblProtein(),
  91           "ENSP00000288602",
  92           ">ENSP00000288602\n"
  93                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  94                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
  95                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
  96                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
  97                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
  98                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
  99                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
 100                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
 101                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
 102                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
 103                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
 104                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
 105                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
 106
 107   @BeforeClass(alwaysRun = true)
 108   public void setUp()
 109   {
 110     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
 111   }
 112
 113   @AfterClass(alwaysRun = true)
 114   public void tearDown()
 115   {
 116     SequenceOntologyFactory.setInstance(null);
 117   }
 118
 119   @DataProvider(name = "ens_seqs")
 120   public Object[][] createData(Method m)
 121   {
 122     System.out.println(m.getName());
 123     return allSeqs;
 124   }
 125
 126   @Test(dataProvider = "ens_seqs", suiteName = "live")
 127   public void testGetOneSeqs(EnsemblRestClient proxy, String sq,
 128           String fastasq) throws Exception
 129   {
 130     FileParse fp = proxy.getSequenceReader(Arrays
 131             .asList(new String[] { sq }));
 132     SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
 133     FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
 134     SequenceI[] trueSqs = trueRes.getSeqsAsArray();
 135     Assert.assertEquals(sqs.length, trueSqs.length,
 136             "Different number of sequences retrieved for query " + sq);
 137     Alignment ral = new Alignment(sqs);
 138     for (SequenceI tr : trueSqs)
 139     {
 140       SequenceI[] rseq;
 141       Assert.assertNotNull(
 142               rseq = ral.findSequenceMatch(tr.getName()),
 143               "Couldn't find sequences matching expected sequence "
 144                       + tr.getName());
 145       Assert.assertEquals(rseq.length, 1,
 146               "Expected only one sequence for sequence ID " + tr.getName());
 147       Assert.assertEquals(
 148               rseq[0].getSequenceAsString(),
 149               tr.getSequenceAsString(),
 150               "Sequences differ for " + tr.getName() + "\n" + "Exp:"
 151                       + tr.getSequenceAsString() + "\n" + "Got:"
 152                       + rseq[0].getSequenceAsString());
 153
 154     }
 155   }
 156
 157   @Test(groups = "Functional")
 158   public void getGenomicRangesFromFeatures()
 159   {
 160
 161   }
 162
 163   @Test(groups = "Functional")
 164   public void testIsTranscriptIdentifier()
 165   {
 166     EnsemblSeqProxy testee = new EnsemblGene();
 167     assertFalse(testee.isTranscriptIdentifier(null));
 168     assertFalse(testee.isTranscriptIdentifier(""));
 169     assertFalse(testee.isTranscriptIdentifier("ENSG00000012345"));
 170     assertTrue(testee.isTranscriptIdentifier("ENST00000012345"));
 171     assertTrue(testee.isTranscriptIdentifier("ENSMUST00000012345"));
 172     assertFalse(testee.isTranscriptIdentifier("enst00000012345"));
 173     assertFalse(testee.isTranscriptIdentifier("ENST000000123456"));
 174     assertFalse(testee.isTranscriptIdentifier("ENST0000001234"));
 175   }
 176
 177   @Test(groups = "Functional")
 178   public void testIsGeneIdentifier()
 179   {
 180     EnsemblSeqProxy testee = new EnsemblGene();
 181     assertFalse(testee.isGeneIdentifier(null));
 182     assertFalse(testee.isGeneIdentifier(""));
 183     assertFalse(testee.isGeneIdentifier("ENST00000012345"));
 184     assertTrue(testee.isGeneIdentifier("ENSG00000012345"));
 185     assertTrue(testee.isGeneIdentifier("ENSMUSG00000012345"));
 186     assertFalse(testee.isGeneIdentifier("ensg00000012345"));
 187     assertFalse(testee.isGeneIdentifier("ENSG000000123456"));
 188     assertFalse(testee.isGeneIdentifier("ENSG0000001234"));
 189   }
 190
 191   /**
 192    * Test the method that appends a single allele's reverse complement to a
 193    * string buffer
 194    */
 195   @Test(groups = "Functional")
 196   public void testReverseComplementAllele()
 197   {
 198     StringBuilder sb = new StringBuilder();
 199     EnsemblSeqProxy.reverseComplementAllele(sb, "G"); // comp=C
 200     EnsemblSeqProxy.reverseComplementAllele(sb, "g"); // comp=c
 201     EnsemblSeqProxy.reverseComplementAllele(sb, "C"); // comp=G
 202     EnsemblSeqProxy.reverseComplementAllele(sb, "T"); // comp=A
 203     EnsemblSeqProxy.reverseComplementAllele(sb, "A"); // comp=T
 204     assertEquals("C,c,G,A,T", sb.toString());
 205
 206     sb = new StringBuilder();
 207     EnsemblSeqProxy.reverseComplementAllele(sb, "-GATt"); // revcomp=aATC-
 208     EnsemblSeqProxy.reverseComplementAllele(sb, "hgmd_mutation");
 209     EnsemblSeqProxy.reverseComplementAllele(sb, "PhenCode_variation");
 210     assertEquals("aATC-,hgmd_mutation,PhenCode_variation", sb.toString());
 211   }
 212
 213   /**
 214    * Test the method that computes the reverse complement of the alleles in a
 215    * sequence_variant feature
 216    */
 217   @Test(groups = "Functional")
 218   public void testReverseComplementAlleles()
 219   {
 220     String alleles = "C,G,-TAC,HGMD_MUTATION,gac";
 221     SequenceFeature sf = new SequenceFeature("sequence_variant", alleles,
 222             1, 2, 0f, null);
 223     sf.setValue("alleles", alleles);
 224     sf.setAttributes("x=y,z;alleles=" + alleles + ";a=b,c");
 225
 226     EnsemblSeqProxy.reverseComplementAlleles(sf);
 227     String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc";
 228     // verify description is updated with reverse complement
 229     assertEquals(revcomp, sf.getDescription());
 230     // verify alleles attribute is updated with reverse complement
 231     assertEquals(revcomp, sf.getValue("alleles"));
 232     // verify attributes string is updated with reverse complement
 233     assertEquals("x=y,z;alleles=" + revcomp + ";a=b,c", sf.getAttributes());
 234   }
 235
 236   @Test(groups = "Functional")
 237   public void testSortFeatures()
 238   {
 239     SequenceFeature sf1 = new SequenceFeature("", "", 10, 15, 0f, null);
 240     SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
 241     SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
 242     SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
 243     SequenceFeature[] sfs = new SequenceFeature[] { sf1, sf2, sf3, sf4 };
 244
 245     // sort by start position ascending (forward strand)
 246     // sf2 and sf3 tie and should not be reordered by sorting
 247     EnsemblSeqProxy.sortFeatures(sfs, true);
 248     assertArrayEquals(new SequenceFeature[] { sf2, sf3, sf1, sf4 }, sfs);
 249
 250     // sort by end position descending (reverse strand)
 251     EnsemblSeqProxy.sortFeatures(sfs, false);
 252     assertArrayEquals(new SequenceFeature[] { sf1, sf3, sf2, sf4 }, sfs);
 253   }
 254 }