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.EnsemblSeqType;
   6 import jalview.io.AppletFormatAdapter;
   7 import jalview.io.FastaFile;
   8 import jalview.io.FileParse;
   9 import jalview.util.DBRefUtils;
  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 EnsemblSeqProxyTest
  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.PROTEIN,
  51           "CCDS5863.1",
  52           ">CCDS5863.1\n"
  53                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  54                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
  55                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
  56                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
  57                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
  58                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
  59                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
  60                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
  61                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
  62                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
  63                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
  64                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
  65                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
  66       {
  67           EnsemblSeqType.TRANSCRIPT,
  68           "CCDS5863.1",
  69           ">CCDS5863.1\n"
  70                   + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
  71                   + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
  72                   + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
  73                   + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
  74                   + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
  75                   + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
  76                   + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
  77                   + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
  78                   + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
  79                   + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
  80                   + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
  81                   + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
  82                   + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
  83                   + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
  84                   + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
  85                   + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
  86                   + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
  87                   + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
  88                   + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
  89                   + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
  90                   + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
  91                   + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
  92                   + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
  93                   + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
  94                   + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
  95                   + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
  96                   + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
  97                   + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
  98                   + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
  99                   + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
 100                   + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
 101                   + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
 102                   + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
 103                   + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
 104                   + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
 105                   + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
 106                   + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
 107                   + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
 108                   + "GGTGCGTTTCCTGTCCACTGA\n" },
 109       {
 110           EnsemblSeqType.PROTEIN,
 111           "ENSP00000288602",
 112           ">ENSP00000288602\n"
 113                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
 114                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
 115                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
 116                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
 117                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
 118                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
 119                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
 120                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
 121                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
 122                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
 123                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
 124                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
 125                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
 126
 127   @Test(dataProvider = "ens_seqs", suiteName = "live")
 128   public void testGetOneSeqs(EnsemblSeqType type, String sq, String fastasq)
 129           throws Exception
 130   {
 131     SeqFetcher sf = new SeqFetcher();
 132     FileParse fp = sf.getSequenceReader(type, Arrays.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 }