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.SequenceI;
   8 import jalview.io.AppletFormatAdapter;
   9 import jalview.io.FastaFile;
  10 import jalview.io.FileParse;
  11
  12 import java.lang.reflect.Method;
  13 import java.net.MalformedURLException;
  14 import java.net.URL;
  15 import java.util.Arrays;
  16 import java.util.List;
  17
  18 import org.testng.Assert;
  19 import org.testng.annotations.DataProvider;
  20 import org.testng.annotations.Test;
  21
  22
  23 public class EnsemblSeqProxyTest
  24 {
  25   private static final Object[][] allSeqs = new Object[][] {
  26       {
  27           new EnsemblProtein(),
  28           "CCDS5863.1",
  29           ">CCDS5863.1\n"
  30                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  31                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
  32                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
  33                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
  34                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
  35                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
  36                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
  37                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
  38                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
  39                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
  40                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
  41                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
  42                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
  43       {
  44           new EnsemblCdna(),
  45           "CCDS5863.1",
  46           ">CCDS5863.1\n"
  47                   + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
  48                   + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
  49                   + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
  50                   + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
  51                   + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
  52                   + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
  53                   + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
  54                   + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
  55                   + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
  56                   + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
  57                   + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
  58                   + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
  59                   + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
  60                   + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
  61                   + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
  62                   + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
  63                   + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
  64                   + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
  65                   + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
  66                   + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
  67                   + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
  68                   + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
  69                   + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
  70                   + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
  71                   + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
  72                   + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
  73                   + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
  74                   + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
  75                   + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
  76                   + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
  77                   + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
  78                   + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
  79                   + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
  80                   + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
  81                   + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
  82                   + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
  83                   + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
  84                   + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
  85                   + "GGTGCGTTTCCTGTCCACTGA\n" },
  86       {
  87           new EnsemblProtein(),
  88           "ENSP00000288602",
  89           ">ENSP00000288602\n"
  90                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  91                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
  92                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
  93                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
  94                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
  95                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
  96                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
  97                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
  98                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
  99                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
 100                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
 101                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
 102                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
 103
 104   @DataProvider(name = "queries")
 105   public Object[][] createQueryData(Method m)
 106   {
 107     return new Object[][] { { "CCDS5863.1" }, { "ENSP00000288602" } };
 108   }
 109
 110   @Test(dataProvider = "queries")
 111   public void testIsValidReference(String query) throws Exception
 112   {
 113     EnsemblSequenceFetcher esq = new EnsemblProtein();
 114     Assert.assertTrue(esq.isValidReference(query),
 115             "Expected reference string " + query
 116                     + " to be valid for regex "
 117                     + esq.getAccessionValidator().toString());
 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(suiteName = "live")
 160   public void testLiveCheckEnsembl()
 161   {
 162     EnsemblRestClient sf = new EnsemblRestClient()
 163     {
 164
 165       @Override
 166       public String getDbName()
 167       {
 168         // TODO Auto-generated method stub
 169         return null;
 170       }
 171
 172       @Override
 173       public AlignmentI getSequenceRecords(String queries) throws Exception
 174       {
 175         // TODO Auto-generated method stub
 176         return null;
 177       }
 178
 179       @Override
 180       protected URL getUrl(List<String> ids) throws MalformedURLException
 181       {
 182         // TODO Auto-generated method stub
 183         return null;
 184       }
 185
 186       @Override
 187       protected boolean useGetRequest()
 188       {
 189         // TODO Auto-generated method stub
 190         return false;
 191       }
 192
 193       @Override
 194       protected String getRequestMimeType(boolean b)
 195       {
 196         // TODO Auto-generated method stub
 197         return null;
 198       }
 199
 200       @Override
 201       protected String getResponseMimeType()
 202       {
 203         // TODO Auto-generated method stub
 204         return null;
 205       }
 206
 207     };
 208     boolean isAvailable = sf.isEnsemblAvailable();
 209     System.out.println("Ensembl is "
 210             + (isAvailable ? "UP!"
 211                     : "DOWN or unreachable ******************* BAD!"));
 212   }
 213
 214   /**
 215    * Tests for the method that computes all peptide variants given codon
 216    * variants
 217    */
 218   @Test(groups = "Functional")
 219   public void testComputePeptideVariants()
 220   {
 221     String[][] codonVariants = new String[][] { { "A" }, { "G" }, { "T" } };
 222
 223     /*
 224      * AGT codes for S - this is not included in the variants returned
 225      */
 226     List<String> variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
 227     assertEquals("[]", variants.toString());
 228
 229     // S is reported if it differs from the current value (A):
 230     variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "A");
 231     assertEquals("[S]", variants.toString());
 232
 233     /*
 234      * synonymous variant is not reported
 235      */
 236     codonVariants = new String[][] { { "A" }, { "G" }, { "C", "T" } };
 237     // AGC and AGT both code for S
 238     variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "s");
 239     assertEquals("[]", variants.toString());
 240
 241     /*
 242      * equivalent variants are only reported once
 243      */
 244     codonVariants = new String[][] { { "C" }, { "T" },
 245         { "A", "C", "G", "T" } };
 246     // CTA CTC CTG CTT all code for L
 247     variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
 248     assertEquals("[L]", variants.toString());
 249
 250     /*
 251      * vary codons 1 and 2; variant products are sorted and non-redundant
 252      */
 253     codonVariants = new String[][] { { "a", "C" }, { "g", "T" }, { "A" } };
 254     // aga ata cga cta code for R, I, R, L
 255     variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
 256     assertEquals("[I, L, R]", variants.toString());
 257
 258     /*
 259      * vary codons 2 and 3
 260      */
 261     codonVariants = new String[][] { { "a" }, { "g", "T" }, { "A", "c" } };
 262     // aga agc ata atc code for R, S, I, I
 263     variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
 264     assertEquals("[I, R]", variants.toString());
 265
 266     /*
 267      * vary codons 1 and 3
 268      */
 269     codonVariants = new String[][] { { "a", "t" }, { "a" }, { "t", "g" } };
 270     // aat aag tat tag code for N, K, Y, STOP - STOP sorted to end
 271     variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
 272     assertEquals("[K, N, Y, STOP]", variants.toString());
 273
 274     /*
 275      * vary codons 1, 2 and 3
 276      */
 277     codonVariants = new String[][] { { "a", "t" }, { "G", "C" },
 278         { "t", "g" } };
 279     // agt agg act acg tgt tgg tct tcg code for S, R, T, T, C, W, S, S
 280     variants = EnsemblSeqProxy.computePeptideVariants(codonVariants, "S");
 281     assertEquals("[C, R, T, W]", variants.toString());
 282   }
 283 }