test/jalview/ext/ensembl/SeqFetcherTest.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
  10 import java.lang.reflect.Method;
  11 import java.util.Arrays;
  12
  13 import org.testng.Assert;
  14 import org.testng.annotations.DataProvider;
  15 import org.testng.annotations.Test;
  16
  17 public class SeqFetcherTest
  18 {
  19   private static final Object[][] allSeqs = new Object[][] {
  20       {
  21           EnsemblSeqType.PROTEIN,
  22           "CCDS5863.1",
  23           ">CCDS5863.1\n"
  24                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  25                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
  26                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
  27                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
  28                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
  29                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
  30                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
  31                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
  32                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
  33                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
  34                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
  35                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
  36                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH\n" },
  37       {
  38           EnsemblSeqType.TRANSCRIPT,
  39           "CCDS5863.1",
  40           ">CCDS5863.1\n"
  41                   + "ATGGCGGCGCTGAGCGGTGGCGGTGGTGGCGGCGCGGAGCCGGGCCAGGCTCTGTTCAAC\n"
  42                   + "GGGGACATGGAGCCCGAGGCCGGCGCCGGCGCCGGCGCCGCGGCCTCTTCGGCTGCGGAC\n"
  43                   + "CCTGCCATTCCGGAGGAGGTGTGGAATATCAAACAAATGATTAAGTTGACACAGGAACAT\n"
  44                   + "ATAGAGGCCCTATTGGACAAATTTGGTGGGGAGCATAATCCACCATCAATATATCTGGAG\n"
  45                   + "GCCTATGAAGAATACACCAGCAAGCTAGATGCACTCCAACAAAGAGAACAACAGTTATTG\n"
  46                   + "GAATCTCTGGGGAACGGAACTGATTTTTCTGTTTCTAGCTCTGCATCAATGGATACCGTT\n"
  47                   + "ACATCTTCTTCCTCTTCTAGCCTTTCAGTGCTACCTTCATCTCTTTCAGTTTTTCAAAAT\n"
  48                   + "CCCACAGATGTGGCACGGAGCAACCCCAAGTCACCACAAAAACCTATCGTTAGAGTCTTC\n"
  49                   + "CTGCCCAACAAACAGAGGACAGTGGTACCTGCAAGGTGTGGAGTTACAGTCCGAGACAGT\n"
  50                   + "CTAAAGAAAGCACTGATGATGAGAGGTCTAATCCCAGAGTGCTGTGCTGTTTACAGAATT\n"
  51                   + "CAGGATGGAGAGAAGAAACCAATTGGTTGGGACACTGATATTTCCTGGCTTACTGGAGAA\n"
  52                   + "GAATTGCATGTGGAAGTGTTGGAGAATGTTCCACTTACAACACACAACTTTGTACGAAAA\n"
  53                   + "ACGTTTTTCACCTTAGCATTTTGTGACTTTTGTCGAAAGCTGCTTTTCCAGGGTTTCCGC\n"
  54                   + "TGTCAAACATGTGGTTATAAATTTCACCAGCGTTGTAGTACAGAAGTTCCACTGATGTGT\n"
  55                   + "GTTAATTATGACCAACTTGATTTGCTGTTTGTCTCCAAGTTCTTTGAACACCACCCAATA\n"
  56                   + "CCACAGGAAGAGGCGTCCTTAGCAGAGACTGCCCTAACATCTGGATCATCCCCTTCCGCA\n"
  57                   + "CCCGCCTCGGACTCTATTGGGCCCCAAATTCTCACCAGTCCGTCTCCTTCAAAATCCATT\n"
  58                   + "CCAATTCCACAGCCCTTCCGACCAGCAGATGAAGATCATCGAAATCAATTTGGGCAACGA\n"
  59                   + "GACCGATCCTCATCAGCTCCCAATGTGCATATAAACACAATAGAACCTGTCAATATTGAT\n"
  60                   + "GACTTGATTAGAGACCAAGGATTTCGTGGTGATGGAGGATCAACCACAGGTTTGTCTGCT\n"
  61                   + "ACCCCCCCTGCCTCATTACCTGGCTCACTAACTAACGTGAAAGCCTTACAGAAATCTCCA\n"
  62                   + "GGACCTCAGCGAGAAAGGAAGTCATCTTCATCCTCAGAAGACAGGAATCGAATGAAAACA\n"
  63                   + "CTTGGTAGACGGGACTCGAGTGATGATTGGGAGATTCCTGATGGGCAGATTACAGTGGGA\n"
  64                   + "CAAAGAATTGGATCTGGATCATTTGGAACAGTCTACAAGGGAAAGTGGCATGGTGATGTG\n"
  65                   + "GCAGTGAAAATGTTGAATGTGACAGCACCTACACCTCAGCAGTTACAAGCCTTCAAAAAT\n"
  66                   + "GAAGTAGGAGTACTCAGGAAAACACGACATGTGAATATCCTACTCTTCATGGGCTATTCC\n"
  67                   + "ACAAAGCCACAACTGGCTATTGTTACCCAGTGGTGTGAGGGCTCCAGCTTGTATCACCAT\n"
  68                   + "CTCCATATCATTGAGACCAAATTTGAGATGATCAAACTTATAGATATTGCACGACAGACT\n"
  69                   + "GCACAGGGCATGGATTACTTACACGCCAAGTCAATCATCCACAGAGACCTCAAGAGTAAT\n"
  70                   + "AATATATTTCTTCATGAAGACCTCACAGTAAAAATAGGTGATTTTGGTCTAGCTACAGTG\n"
  71                   + "AAATCTCGATGGAGTGGGTCCCATCAGTTTGAACAGTTGTCTGGATCCATTTTGTGGATG\n"
  72                   + "GCACCAGAAGTCATCAGAATGCAAGATAAAAATCCATACAGCTTTCAGTCAGATGTATAT\n"
  73                   + "GCATTTGGAATTGTTCTGTATGAATTGATGACTGGACAGTTACCTTATTCAAACATCAAC\n"
  74                   + "AACAGGGACCAGATAATTTTTATGGTGGGACGAGGATACCTGTCTCCAGATCTCAGTAAG\n"
  75                   + "GTACGGAGTAACTGTCCAAAAGCCATGAAGAGATTAATGGCAGAGTGCCTCAAAAAGAAA\n"
  76                   + "AGAGATGAGAGACCACTCTTTCCCCAAATTCTCGCCTCTATTGAGCTGCTGGCCCGCTCA\n"
  77                   + "TTGCCAAAAATTCACCGCAGTGCATCAGAACCCTCCTTGAATCGGGCTGGTTTCCAAACA\n"
  78                   + "GAGGATTTTAGTCTATATGCTTGTGCTTCTCCAAAAACACCCATCCAGGCAGGGGGATAT\n"
  79                   + "GGTGCGTTTCCTGTCCACTGA\n" },
  80       {
  81           EnsemblSeqType.PROTEIN,
  82           "ENSP00000288602",
  83           ">ENSP00000288602\n"
  84                   + "MAALSGGGGGGAEPGQALFNGDMEPEAGAGAGAAASSAADPAIPEEVWNIKQMIKLTQEH\n"
  85                   + "IEALLDKFGGEHNPPSIYLEAYEEYTSKLDALQQREQQLLESLGNGTDFSVSSSASMDTV\n"
  86                   + "TSSSSSSLSVLPSSLSVFQNPTDVARSNPKSPQKPIVRVFLPNKQRTVVPARCGVTVRDS\n"
  87                   + "LKKALMMRGLIPECCAVYRIQDGEKKPIGWDTDISWLTGEELHVEVLENVPLTTHNFVRK\n"
  88                   + "TFFTLAFCDFCRKLLFQGFRCQTCGYKFHQRCSTEVPLMCVNYDQLDLLFVSKFFEHHPI\n"
  89                   + "PQEEASLAETALTSGSSPSAPASDSIGPQILTSPSPSKSIPIPQPFRPADEDHRNQFGQR\n"
  90                   + "DRSSSAPNVHINTIEPVNIDDLIRDQGFRGDGGSTTGLSATPPASLPGSLTNVKALQKSP\n"
  91                   + "GPQRERKSSSSSEDRNRMKTLGRRDSSDDWEIPDGQITVGQRIGSGSFGTVYKGKWHGDV\n"
  92                   + "AVKMLNVTAPTPQQLQAFKNEVGVLRKTRHVNILLFMGYSTKPQLAIVTQWCEGSSLYHH\n"
  93                   + "LHIIETKFEMIKLIDIARQTAQGMDYLHAKSIIHRDLKSNNIFLHEDLTVKIGDFGLATV\n"
  94                   + "KSRWSGSHQFEQLSGSILWMAPEVIRMQDKNPYSFQSDVYAFGIVLYELMTGQLPYSNIN\n"
  95                   + "NRDQIIFMVGRGYLSPDLSKVRSNCPKAMKRLMAECLKKKRDERPLFPQILASIELLARS\n"
  96                   + "LPKIHRSASEPSLNRAGFQTEDFSLYACASPKTPIQAGGYGAFPVH" } };
  97
  98   @DataProvider(name = "ens_seqs")
  99   public Object[][] createData(Method m)
 100   {
 101     System.out.println(m.getName());
 102     return allSeqs;
 103   }
 104
 105   @Test(dataProvider = "ens_seqs", suiteName = "live")
 106   public void testGetOneSeqs(EnsemblSeqType type, String sq, String fastasq)
 107           throws Exception
 108   {
 109     SeqFetcher sf = new SeqFetcher();
 110     FileParse fp = sf.getSequenceReader(type, Arrays.asList(new String[]
 111     { sq }));
 112     SequenceI[] sqs = new FastaFile(fp).getSeqsAsArray();
 113     FastaFile trueRes = new FastaFile(fastasq, AppletFormatAdapter.PASTE);
 114     SequenceI[] trueSqs = trueRes.getSeqsAsArray();
 115     Assert.assertEquals(sqs.length, trueSqs.length,
 116             "Different number of sequences retrieved for query " + sq);
 117     Alignment ral = new Alignment(sqs);
 118     for (SequenceI tr : trueSqs)
 119     {
 120       SequenceI[] rseq;
 121       Assert.assertNotNull(
 122               rseq = ral.findSequenceMatch(tr.getName()),
 123               "Couldn't find sequences matching expected sequence "
 124                       + tr.getName());
 125       Assert.assertEquals(rseq.length, 1,
 126               "Expected only one sequence for sequence ID " + tr.getName());
 127       Assert.assertEquals(
 128               rseq[0].getSequenceAsString(),
 129               tr.getSequenceAsString(),
 130               "Sequences differ for " + tr.getName() + "\n" + "Exp:"
 131                       + tr.getSequenceAsString() + "\n" + "Got:"
 132                       + rseq[0].getSequenceAsString());
 133
 134     }
 135   }
 136
 137   @Test(suiteName = "live")
 138   public void testLiveCheckEnsembl()
 139   {
 140     SeqFetcher sf = new SeqFetcher();
 141     boolean isAvailable = sf.isEnsemblAvailable();
 142     System.out.println("Ensembl is "
 143             + (isAvailable ? "UP!"
 144                     : "DOWN or unreachable ******************* BAD!"));
 145   }
 146   // TODO:
 147   // sequence query with ENSG and anything other than a genomic type will yield
 148   // sequences with different IDs which will
 149   // break the post-processing stage where DBRefs are assigned to sequences.
 150   // -> multiple_sequences = true is needed additional parameter
 151   // http://rest.ensembl.org/sequence/id/ENSG00000157764?content-type=text/x-json;type=protein;multiple_sequences=true
 152   // result with four transcripts, cds, cdna, and protein products.
 153   // *
 154   // features for ENG -
 155   // http://rest.ensembl.org/overlap/id/ENSG00000157764?feature=cds&feature=exon&feature=transcript&content-type=text/x-gff3
 156   // transcript: gives locus, all transcript products with ENSG parents
 157   // gene: give all ENSG on locus
 158   // exon: all exon boundaries. CDS same info.
 159
 160   // @Test(dataProvider = "ens_seqs", suiteName = "live")
 161   // public void testGetOneSeqs(EnsemblSeqType type, String sq, String fastasq)
 162   // throws Exception
 163   // {
 164   //
 165   // {
 166   // Assert.assertTrue(rseq[0].getDBRef() != null
 167   // && rseq[0].getDBRef().length > 0,
 168   // "No database references added to sequence by fetcher.");
 169   // Assert.assertNotNull(DBRefUtils.searchRefs(rseq[0].getDBRef(),
 170   // new DBRefEntry("ENSEMBL", null, sq)),
 171   // "Could't find database references added to sequence by fetcher.");
 172   //
 173   // }
 174
 175 }