test/jalview/ext/ensembl/EnsemblSeqProxyTest.java

   1 package jalview.ext.ensembl;
   2
   3 import static org.testng.AssertJUnit.assertEquals;
   4
   5 import jalview.datamodel.Alignment;
   6 import jalview.datamodel.AlignmentI;
   7 import jalview.datamodel.Sequence;
   8 import jalview.datamodel.SequenceFeature;
   9 import jalview.datamodel.SequenceI;
  10 import jalview.io.AppletFormatAdapter;
  11 import jalview.io.FastaFile;
  12 import jalview.io.FileParse;
  13 import jalview.io.gff.SequenceOntologyFactory;
  14 import jalview.io.gff.SequenceOntologyLite;
  15
  16 import java.lang.reflect.Method;
  17 import java.net.MalformedURLException;
  18 import java.net.URL;
  19 import java.util.ArrayList;
  20 import java.util.Arrays;
  21 import java.util.List;
  22
  23 import org.testng.Assert;
  24 import org.testng.annotations.AfterClass;
  25 import org.testng.annotations.BeforeClass;
  26 import org.testng.annotations.DataProvider;
  27 import org.testng.annotations.Test;
  28
  29
  30 public class EnsemblSeqProxyTest
  31 {
  32   private static final Object[][] allSeqs = new Object[][] {
  33       {
  34           new EnsemblProtein(),
  35           "CCDS5863.1",
  36           ">CCDS5863.1\n"
  37                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  38                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
  39                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
  40                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
  41                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
  42                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
  43                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
  44                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
  45                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
  46                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
  47                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
  48                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
  49                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
  50       {
  51           new EnsemblCdna(),
  52           "CCDS5863.1",
  53           ">CCDS5863.1\n"
  54                   + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
  55                   + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
  56                   + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
  57                   + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
  58                   + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
  59                   + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
  60                   + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
  61                   + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
  62                   + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
  63                   + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
  64                   + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
  65                   + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
  66                   + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
  67                   + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
  68                   + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
  69                   + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
  70                   + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
  71                   + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
  72                   + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
  73                   + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
  74                   + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
  75                   + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
  76                   + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
  77                   + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
  78                   + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
  79                   + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
  80                   + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
  81                   + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
  82                   + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
  83                   + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
  84                   + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
  85                   + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
  86                   + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
  87                   + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
  88                   + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
  89                   + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
  90                   + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
  91                   + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
  92                   + "GGTGCGTTTCCTGTCCACTGA\n" },
  93       {
  94           new EnsemblProtein(),
  95           "ENSP00000288602",
  96           ">ENSP00000288602\n"
  97                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  98                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
  99                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
 100                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
 101                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
 102                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
 103                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
 104                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
 105                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
 106                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
 107                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
 108                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
 109                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
 110
 111   @BeforeClass
 112   public void setUp()
 113   {
 114     SequenceOntologyFactory.setInstance(new SequenceOntologyLite());
 115   }
 116
 117   @AfterClass
 118   public void tearDown()
 119   {
 120     SequenceOntologyFactory.setInstance(null);
 121   }
 122
 123   @DataProvider(name = "ens_seqs")
 124   public Object[][] createData(Method m)
 125   {
 126     System.out.println(m.getName());
 127     return allSeqs;
 128   }
 129
 130   @Test(dataProvider = "ens_seqs", suiteName = "live")
 131   public void testGetOneSeqs(EnsemblRestClient proxy, String sq, String fastasq)
 132           throws Exception
 133   {
 134     FileParse fp = proxy.getSequenceReader(Arrays
 135             .asList(new String[]
 136     { sq }));
 137     SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
 138     FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
 139     SequenceI[] trueSqs = trueRes.getSeqsAsArray();
 140     Assert.assertEquals(sqs.length, trueSqs.length,
 141             "Different number of sequences retrieved for query " + sq);
 142     Alignment ral = new Alignment(sqs);
 143     for (SequenceI tr : trueSqs)
 144     {
 145       SequenceI[] rseq;
 146       Assert.assertNotNull(
 147               rseq = ral.findSequenceMatch(tr.getName()),
 148               "Couldn't find sequences matching expected sequence "
 149                       + tr.getName());
 150       Assert.assertEquals(rseq.length, 1,
 151               "Expected only one sequence for sequence ID " + tr.getName());
 152       Assert.assertEquals(
 153               rseq[0].getSequenceAsString(),
 154               tr.getSequenceAsString(),
 155               "Sequences differ for " + tr.getName() + "\n" + "Exp:"
 156                       + tr.getSequenceAsString() + "\n" + "Got:"
 157                       + rseq[0].getSequenceAsString());
 158
 159     }
 160   }
 161
 162   @Test(suiteName = "live")
 163   public void testLiveCheckEnsembl()
 164   {
 165     EnsemblRestClient sf = new EnsemblRestClient()
 166     {
 167
 168       @Override
 169       public String getDbName()
 170       {
 171         // TODO Auto-generated method stub
 172         return null;
 173       }
 174
 175       @Override
 176       public AlignmentI getSequenceRecords(String queries) throws Exception
 177       {
 178         // TODO Auto-generated method stub
 179         return null;
 180       }
 181
 182       @Override
 183       protected URL getUrl(List<String> ids) throws MalformedURLException
 184       {
 185         // TODO Auto-generated method stub
 186         return null;
 187       }
 188
 189       @Override
 190       protected boolean useGetRequest()
 191       {
 192         // TODO Auto-generated method stub
 193         return false;
 194       }
 195
 196       @Override
 197       protected String getRequestMimeType(boolean b)
 198       {
 199         // TODO Auto-generated method stub
 200         return null;
 201       }
 202
 203       @Override
 204       protected String getResponseMimeType()
 205       {
 206         // TODO Auto-generated method stub
 207         return null;
 208       }
 209
 210     };
 211     boolean isAvailable = sf.isEnsemblAvailable();
 212     System.out.println("Ensembl is "
 213             + (isAvailable ? "UP!"
 214                     : "DOWN or unreachable ******************* BAD!"));
 215   }
 216
 217   /**
 218    * Tests for the method that computes all peptide variants given codon
 219    * variants
 220    */
 221   @Test(groups = "Functional")
 222   public void testComputePeptideVariants()
 223   {
 224     String[][] codonVariants = new String[][] { { "A" }, { "G" }, { "T" } };
 225
 226     /*
 227      * AGT codes for S - this is not included in the variants returned
 228      */
 229     List<String> variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
 230     assertEquals("[]", variants.toString());
 231
 232     // S is reported if it differs from the current value (A):
 233     variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "A");
 234     assertEquals("[S]", variants.toString());
 235
 236     /*
 237      * synonymous variant is not reported
 238      */
 239     codonVariants = new String[][] { { "A" }, { "G" }, { "C", "T" } };
 240     // AGC and AGT both code for S
 241     variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "s");
 242     assertEquals("[]", variants.toString());
 243
 244     /*
 245      * equivalent variants are only reported once
 246      */
 247     codonVariants = new String[][] { { "C" }, { "T" },
 248         { "A", "C", "G", "T" } };
 249     // CTA CTC CTG CTT all code for L
 250     variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
 251     assertEquals("[L]", variants.toString());
 252
 253     /*
 254      * vary codons 1 and 2; variant products are sorted and non-redundant
 255      */
 256     codonVariants = new String[][] { { "a", "C" }, { "g", "T" }, { "A" } };
 257     // aga ata cga cta code for R, I, R, L
 258     variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
 259     assertEquals("[I, L, R]", variants.toString());
 260
 261     /*
 262      * vary codons 2 and 3
 263      */
 264     codonVariants = new String[][] { { "a" }, { "g", "T" }, { "A", "c" } };
 265     // aga agc ata atc code for R, S, I, I
 266     variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
 267     assertEquals("[I, R]", variants.toString());
 268
 269     /*
 270      * vary codons 1 and 3
 271      */
 272     codonVariants = new String[][] { { "a", "t" }, { "a" }, { "t", "g" } };
 273     // aat aag tat tag code for N, K, Y, STOP - STOP sorted to end
 274     variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
 275     assertEquals("[K, N, Y, STOP]", variants.toString());
 276
 277     /*
 278      * vary codons 1, 2 and 3
 279      */
 280     codonVariants = new String[][] { { "a", "t" }, { "G", "C" },
 281         { "t", "g" } };
 282     // agt agg act acg tgt tgg tct tcg code for S, R, T, T, C, W, S, S
 283     variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
 284     assertEquals("[C, R, T, W]", variants.toString());
 285   }
 286
 287   /**
 288    * Tests for the method that maps the subset of a dna sequence that has CDS
 289    * (or subtype) feature.
 290    */
 291   @Test(groups = "Functional")
 292   public void testGetCdsRanges()
 293   {
 294     EnsemblSeqProxy testee = new EnsemblSeqProxyAdapter();
 295
 296     SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
 297     dnaSeq.createDatasetSequence();
 298     SequenceI ds = dnaSeq.getDatasetSequence();
 299
 300     // CDS for dna 3-6
 301     SequenceFeature sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
 302     ds.addSequenceFeature(sf);
 303     // exon feature should be ignored here
 304     sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
 305     ds.addSequenceFeature(sf);
 306     // CDS for dna 10-12
 307     sf = new SequenceFeature("CDS_predicted", "", 10, 12, 0f, null);
 308     ds.addSequenceFeature(sf);
 309
 310     List<int[]> ranges = new ArrayList<int[]>();
 311     int mappedLength = testee.getCdsRanges(dnaSeq, ranges);
 312     assertEquals(6, mappedLength);
 313     assertEquals(2, ranges.size());
 314     assertEquals(4, ranges.get(0)[0]);
 315     assertEquals(6, ranges.get(0)[1]);
 316     assertEquals(10, ranges.get(1)[0]);
 317     assertEquals(12, ranges.get(1)[1]);
 318
 319   }
 320
 321   @Test(groups = "Functional")
 322   public void getGenomicRangesFromFeatures()
 323   {
 324
 325   }
 326
 327   /**
 328    * Tests for the method that maps the subset of a dna sequence that has CDS
 329    * (or subtype) feature - case where the start codon is incomplete.
 330    */
 331   @Test(groups = "Functional")
 332   public void testGetCdsRanges_fivePrimeIncomplete()
 333   {
 334     EnsemblSeqProxy testee = new EnsemblSeqProxyAdapter();
 335
 336     SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
 337     dnaSeq.createDatasetSequence();
 338     SequenceI ds = dnaSeq.getDatasetSequence();
 339
 340     // CDS for dna 5-6 (incomplete codon), 7-9
 341     SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
 342     sf.setPhase("2"); // skip 2 bases to start of next codon
 343     ds.addSequenceFeature(sf);
 344     ds.addSequenceFeature(sf);
 345     // CDS for dna 13-15
 346     sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
 347     ds.addSequenceFeature(sf);
 348
 349     List<int[]> ranges = new ArrayList<int[]>();
 350     int mappedLength = testee.getCdsRanges(dnaSeq, ranges);
 351
 352     /*
 353      * check the mapping starts with the first complete codon
 354      */
 355     assertEquals(6, mappedLength);
 356     assertEquals(2, ranges.size());
 357     assertEquals(7, ranges.get(0)[0]);
 358     assertEquals(9, ranges.get(0)[1]);
 359     assertEquals(13, ranges.get(1)[0]);
 360     assertEquals(15, ranges.get(1)[1]);
 361   }
 362 }