test/jalview/ext/ensembl/EnsemblSeqProxyTest.java

   1 package jalview.ext.ensembl;
   2
   3 import static org.testng.AssertJUnit.assertEquals;
   4 import static org.testng.AssertJUnit.assertFalse;
   5 import static org.testng.AssertJUnit.assertTrue;
   6
   7 import jalview.analysis.AlignmentUtils;
   8 import jalview.datamodel.Alignment;
   9 import jalview.datamodel.AlignmentI;
  10 import jalview.datamodel.SequenceI;
  11 import jalview.io.AppletFormatAdapter;
  12 import jalview.io.FastaFile;
  13 import jalview.io.FileParse;
  14 import jalview.io.gff.SequenceOntologyFactory;
  15 import jalview.io.gff.SequenceOntologyLite;
  16
  17 import java.lang.reflect.Method;
  18 import java.net.MalformedURLException;
  19 import java.net.URL;
  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   @Test(groups = "Functional")
 218   public void getGenomicRangesFromFeatures()
 219   {
 220
 221   }
 222
 223   @Test(groups = "Functional")
 224   public void testIsTranscriptIdentifier()
 225   {
 226     EnsemblSeqProxy testee = new EnsemblGene();
 227     assertFalse(testee.isTranscriptIdentifier(null));
 228     assertFalse(testee.isTranscriptIdentifier(""));
 229     assertFalse(testee.isTranscriptIdentifier("ENSG00000012345"));
 230     assertTrue(testee.isTranscriptIdentifier("ENST00000012345"));
 231     assertTrue(testee.isTranscriptIdentifier("ENSMUST00000012345"));
 232     assertFalse(testee.isTranscriptIdentifier("enst00000012345"));
 233     assertFalse(testee.isTranscriptIdentifier("ENST000000123456"));
 234     assertFalse(testee.isTranscriptIdentifier("ENST0000001234"));
 235   }
 236
 237   @Test(groups = "Functional")
 238   public void testIsGeneIdentifier()
 239   {
 240     EnsemblSeqProxy testee = new EnsemblGene();
 241     assertFalse(testee.isGeneIdentifier(null));
 242     assertFalse(testee.isGeneIdentifier(""));
 243     assertFalse(testee.isGeneIdentifier("ENST00000012345"));
 244     assertTrue(testee.isGeneIdentifier("ENSG00000012345"));
 245     assertTrue(testee.isGeneIdentifier("ENSMUSG00000012345"));
 246     assertFalse(testee.isGeneIdentifier("ensg00000012345"));
 247     assertFalse(testee.isGeneIdentifier("ENSG000000123456"));
 248     assertFalse(testee.isGeneIdentifier("ENSG0000001234"));
 249   }
 250 }