test/jalview/ext/ensembl/EnsemblSeqProxyTest.java

   1 package jalview.ext.ensembl;
   2
   3 import jalview.datamodel.Alignment;
   4 import jalview.datamodel.SequenceI;
   5 import jalview.ext.ensembl.SeqFetcher;
   6 import jalview.ext.ensembl.SeqFetcher.EnsemblSeqType;
   7 import jalview.io.AppletFormatAdapter;
   8 import jalview.io.FastaFile;
   9 import jalview.io.FileParse;
  10
  11 import java.lang.reflect.Method;
  12 import java.util.Arrays;
  13
  14 import org.testng.Assert;
  15 import org.testng.annotations.DataProvider;
  16 import org.testng.annotations.Test;
  17
  18 public class SeqFetcherTest
  19 {
  20   @Test
  21   public void testCheckEnsembl()
  22   {
  23     SeqFetcher sf = new SeqFetcher();
  24     sf.setTestEnsemblStatus(true);
  25     sf.setTesting(true);
  26     Assert.assertTrue(sf.isEnsemblAvailable());
  27     sf.setTestEnsemblStatus(false);
  28     Assert.assertFalse(sf.isEnsemblAvailable());
  29   }
  30
  31   @Test(suiteName = "live")
  32   public void testLiveCheckEnsembl()
  33   {
  34     SeqFetcher sf = new SeqFetcher();
  35     boolean isAvailable = sf.isEnsemblAvailable();
  36     System.out.println("Ensembl is "
  37             + (isAvailable ? "UP!" : "DOWN ******************* BAD!"));
  38   }
  39
  40   @DataProvider(name = "ens_seqs")
  41   public Object[][] createData(Method m)
  42   {
  43     System.out.println(m.getName());
  44     return allSeqs;
  45   }
  46
  47   public static Object[][] allSeqs = new Object[][]
  48   {
  49   {
  50       EnsemblSeqType.CDS,
  51       "CCDS5863.1",
  52       ">CCDS5863.1\n"
  53               + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
  54               + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
  55               + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
  56               + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
  57               + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
  58               + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
  59               + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
  60               + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
  61               + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
  62               + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
  63               + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
  64               + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
  65               + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
  66               + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
  67               + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
  68               + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
  69               + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
  70               + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
  71               + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
  72               + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
  73               + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
  74               + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
  75               + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
  76               + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
  77               + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
  78               + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
  79               + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
  80               + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
  81               + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
  82               + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
  83               + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
  84               + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
  85               + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
  86               + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
  87               + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
  88               + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
  89               + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
  90               + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
  91               + "GGTGCGTTTCCTGTCCACTGA" } };
  92
  93   @Test(dataProvider = "ens_seqs", suiteName = "live")
  94   public void testGetOneSeqs(EnsemblSeqType type, String sq, String fastasq)
  95           throws Exception
  96   {
  97     SeqFetcher sf = new SeqFetcher();
  98     FileParse fp = sf.getSequenceReader(type, Arrays.asList(new String[]
  99     { sq }));
 100     SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
 101     FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
 102     SequenceI[] trueSqs = trueRes.getSeqsAsArray();
 103     Assert.assertEquals(sqs.length, trueSqs.length,
 104             "Different number of sequences retrieved for query " + sq);
 105     Alignment ral = new Alignment(sqs);
 106     for (SequenceI tr : trueSqs)
 107     {
 108       SequenceI[] rseq;
 109       Assert.assertNotNull(
 110               rseq = ral.findSequenceMatch(tr.getName()),
 111               "Couldn't find sequences matching expected sequence "
 112                       + tr.getName());
 113       Assert.assertEquals(rseq.length, 1,
 114               "Expected only one sequence for sequence ID " + tr.getName());
 115       Assert.assertEquals(
 116               rseq[0].getSequenceAsString(),
 117               tr.getSequenceAsString(),
 118               "Sequences differ for " + tr.getName() + "\n" + "Exp:"
 119                       + tr.getSequenceAsString() + "\n" + "Got:"
 120                       + rseq[0].getSequenceAsString());
 121     }
 122   }
 123 }