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.AlignmentI;
  10 import jalview.datamodel.SequenceFeature;
  11 import jalview.datamodel.SequenceI;
  12 import jalview.io.AppletFormatAdapter;
  13 import jalview.io.FastaFile;
  14 import jalview.io.FileParse;
  15 import jalview.io.gff.SequenceOntologyFactory;
  16 import jalview.io.gff.SequenceOntologyLite;
  17
  18 import java.lang.reflect.Method;
  19 import java.net.MalformedURLException;
  20 import java.net.URL;
  21 import java.util.Arrays;
  22 import java.util.List;
  23
  24 import org.testng.Assert;
  25 import org.testng.annotations.AfterClass;
  26 import org.testng.annotations.BeforeClass;
  27 import org.testng.annotations.DataProvider;
  28 import org.testng.annotations.Test;
  29
  30
  31 public class EnsemblSeqProxyTest
  32 {
  33   private static final Object[][] allSeqs = new Object[][] {
  34       {
  35           new EnsemblProtein(),
  36           "CCDS5863.1",
  37           ">CCDS5863.1\n"
  38                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  39                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
  40                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
  41                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
  42                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
  43                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
  44                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
  45                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
  46                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
  47                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
  48                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
  49                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
  50                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
  51       {
  52           new EnsemblCdna(),
  53           "CCDS5863.1",
  54           ">CCDS5863.1\n"
  55                   + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
  56                   + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
  57                   + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
  58                   + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
  59                   + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
  60                   + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
  61                   + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
  62                   + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
  63                   + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
  64                   + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
  65                   + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
  66                   + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
  67                   + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
  68                   + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
  69                   + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
  70                   + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
  71                   + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
  72                   + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
  73                   + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
  74                   + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
  75                   + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
  76                   + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
  77                   + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
  78                   + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
  79                   + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
  80                   + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
  81                   + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
  82                   + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
  83                   + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
  84                   + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
  85                   + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
  86                   + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
  87                   + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
  88                   + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
  89                   + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
  90                   + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
  91                   + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
  92                   + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
  93                   + "GGTGCGTTTCCTGTCCACTGA\n" },
  94       {
  95           new EnsemblProtein(),
  96           "ENSP00000288602",
  97           ">ENSP00000288602\n"
  98                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  99                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
 100                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
 101                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
 102                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
 103                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
 104                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
 105                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
 106                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
 107                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
 108                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
 109                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
 110                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
 111
 112   @BeforeClass
 113   public void setUp()
 114   {
 115     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
 116   }
 117
 118   @AfterClass
 119   public void tearDown()
 120   {
 121     SequenceOntologyFactory.setInstance(null);
 122   }
 123
 124   @DataProvider(name = "ens_seqs")
 125   public Object[][] createData(Method m)
 126   {
 127     System.out.println(m.getName());
 128     return allSeqs;
 129   }
 130
 131   @Test(dataProvider = "ens_seqs", suiteName = "live")
 132   public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq)
 133           throws Exception
 134   {
 135     FileParse fp = proxy.getSequenceReader(Arrays
 136             .asList(new String[]
 137     { sq }));
 138     SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
 139     FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
 140     SequenceI[] trueSqs = trueRes.getSeqsAsArray();
 141     Assert.assertEquals(sqs.length, trueSqs.length,
 142             "Different number of sequences retrieved for query " + sq);
 143     Alignment ral = new Alignment(sqs);
 144     for (SequenceI tr : trueSqs)
 145     {
 146       SequenceI[] rseq;
 147       Assert.assertNotNull(
 148               rseq = ral.findSequenceMatch(tr.getName()),
 149               "Couldn't find sequences matching expected sequence "
 150                       + tr.getName());
 151       Assert.assertEquals(rseq.length, 1,
 152               "Expected only one sequence for sequence ID " + tr.getName());
 153       Assert.assertEquals(
 154               rseq[0].getSequenceAsString(),
 155               tr.getSequenceAsString(),
 156               "Sequences differ for " + tr.getName() + "\n" + "Exp:"
 157                       + tr.getSequenceAsString() + "\n" + "Got:"
 158                       + rseq[0].getSequenceAsString());
 159
 160     }
 161   }
 162
 163   @Test(suiteName = "live")
 164   public void testLiveCheckEnsembl()
 165   {
 166     EnsemblRestClient sf = new EnsemblRestClient()
 167     {
 168
 169       @Override
 170       public String getDbName()
 171       {
 172         // TODO Auto-generated method stub
 173         return null;
 174       }
 175
 176       @Override
 177       public AlignmentI getSequenceRecords(String queries) throws Exception
 178       {
 179         // TODO Auto-generated method stub
 180         return null;
 181       }
 182
 183       @Override
 184       protected URL getUrl(List<String> ids) throws MalformedURLException
 185       {
 186         // TODO Auto-generated method stub
 187         return null;
 188       }
 189
 190       @Override
 191       protected boolean useGetRequest()
 192       {
 193         // TODO Auto-generated method stub
 194         return false;
 195       }
 196
 197       @Override
 198       protected String getRequestMimeType(boolean b)
 199       {
 200         // TODO Auto-generated method stub
 201         return null;
 202       }
 203
 204       @Override
 205       protected String getResponseMimeType()
 206       {
 207         // TODO Auto-generated method stub
 208         return null;
 209       }
 210
 211     };
 212     boolean isAvailable = sf.isEnsemblAvailable();
 213     System.out.println("Ensembl is "
 214             + (isAvailable ? "UP!"
 215                     : "DOWN or unreachable ******************* BAD!"));
 216   }
 217
 218   @Test(groups = "Functional")
 219   public void getGenomicRangesFromFeatures()
 220   {
 221
 222   }
 223
 224   @Test(groups = "Functional")
 225   public void testIsTranscriptIdentifier()
 226   {
 227     EnsemblSeqProxy testee = new EnsemblGene();
 228     assertFalse(testee.isTranscriptIdentifier(null));
 229     assertFalse(testee.isTranscriptIdentifier(""));
 230     assertFalse(testee.isTranscriptIdentifier("ENSG00000012345"));
 231     assertTrue(testee.isTranscriptIdentifier("ENST00000012345"));
 232     assertTrue(testee.isTranscriptIdentifier("ENSMUST00000012345"));
 233     assertFalse(testee.isTranscriptIdentifier("enst00000012345"));
 234     assertFalse(testee.isTranscriptIdentifier("ENST000000123456"));
 235     assertFalse(testee.isTranscriptIdentifier("ENST0000001234"));
 236   }
 237
 238   @Test(groups = "Functional")
 239   public void testIsGeneIdentifier()
 240   {
 241     EnsemblSeqProxy testee = new EnsemblGene();
 242     assertFalse(testee.isGeneIdentifier(null));
 243     assertFalse(testee.isGeneIdentifier(""));
 244     assertFalse(testee.isGeneIdentifier("ENST00000012345"));
 245     assertTrue(testee.isGeneIdentifier("ENSG00000012345"));
 246     assertTrue(testee.isGeneIdentifier("ENSMUSG00000012345"));
 247     assertFalse(testee.isGeneIdentifier("ensg00000012345"));
 248     assertFalse(testee.isGeneIdentifier("ENSG000000123456"));
 249     assertFalse(testee.isGeneIdentifier("ENSG0000001234"));
 250   }
 251
 252   /**
 253    * Test the method that appends a single allele's reverse complement to a
 254    * string buffer
 255    */
 256   @Test(groups = "Functional")
 257   public void testReverseComplementAllele()
 258   {
 259     StringBuilder sb = new StringBuilder();
 260     EnsemblSeqProxy.reverseComplementAllele(sb, "G"); // comp=C
 261     EnsemblSeqProxy.reverseComplementAllele(sb, "g"); // comp=c
 262     EnsemblSeqProxy.reverseComplementAllele(sb, "C"); // comp=G
 263     EnsemblSeqProxy.reverseComplementAllele(sb, "T"); // comp=A
 264     EnsemblSeqProxy.reverseComplementAllele(sb, "A"); // comp=T
 265     assertEquals("C,c,G,A,T", sb.toString());
 266
 267     sb = new StringBuilder();
 268     EnsemblSeqProxy.reverseComplementAllele(sb, "-GATt"); // revcomp=aATC-
 269     EnsemblSeqProxy.reverseComplementAllele(sb, "hgmd_mutation");
 270     assertEquals("aATC-,hgmd_mutation", sb.toString());
 271   }
 272
 273   /**
 274    * Test the method that computes the reverse complement of the alleles in a
 275    * sequence_variant feature
 276    */
 277   @Test(groups = "Functional")
 278   public void testReverseComplementAlleles()
 279   {
 280     String alleles = "C,G,-TAC,HGMD_MUTATION,gac";
 281     SequenceFeature sf = new SequenceFeature("sequence_variant", alleles,
 282             1, 2, 0f, null);
 283     sf.setValue("alleles", alleles);
 284     sf.setAttributes("x=y,z;alleles=" + alleles + ";a=b,c");
 285
 286     EnsemblSeqProxy.reverseComplementAlleles(sf);
 287     String revcomp = "G,C,GTA-,HGMD_MUTATION,gtc";
 288     // verify description is updated with reverse complement
 289     assertEquals(revcomp, sf.getDescription());
 290     // verify alleles attribute is updated with reverse complement
 291     assertEquals(revcomp, sf.getValue("alleles"));
 292     // verify attributes string is updated with reverse complement
 293     assertEquals("x=y,z;alleles=" + revcomp + ";a=b,c", sf.getAttributes());
 294   }
 295
 296   @Test(groups = "Functional")
 297   public void testSortFeatures()
 298   {
 299     SequenceFeature sf1 = new SequenceFeature("", "", 10, 15, 0f, null);
 300     SequenceFeature sf2 = new SequenceFeature("", "", 8, 12, 0f, null);
 301     SequenceFeature sf3 = new SequenceFeature("", "", 8, 13, 0f, null);
 302     SequenceFeature sf4 = new SequenceFeature("", "", 11, 11, 0f, null);
 303     SequenceFeature[] sfs = new SequenceFeature[] { sf1, sf2, sf3, sf4 };
 304
 305     // sort by start position ascending (forward strand)
 306     // sf2 and sf3 tie and should not be reordered by sorting
 307     EnsemblSeqProxy.sortFeatures(sfs, true);
 308     assertArrayEquals(new SequenceFeature[] { sf2, sf3, sf1, sf4 }, sfs);
 309
 310     // sort by end position descending (reverse strand)
 311     EnsemblSeqProxy.sortFeatures(sfs, false);
 312     assertArrayEquals(new SequenceFeature[] { sf1, sf3, sf2, sf4 }, sfs);
 313   }
 314 }