test/jalview/ws/dbsources/UniprotTest.java

   1 package jalview.ws.dbsources;
   2
   3 import static org.junit.Assert.assertEquals;
   4 import static org.junit.Assert.assertNotNull;
   5 import static org.junit.Assert.assertNull;
   6 import jalview.datamodel.AlignmentI;
   7 import jalview.datamodel.PDBEntry;
   8 import jalview.datamodel.SequenceFeature;
   9 import jalview.datamodel.UniprotEntry;
  10
  11 import java.io.Reader;
  12 import java.io.StringReader;
  13 import java.util.Vector;
  14
  15 import org.junit.Test;
  16
  17 public class UniprotTest
  18 {
  19   // adapted from http://www.uniprot.org/uniprot/A9CKP4.xml
  20   private static final String UNIPROT_XML = "<?xml version='1.0' encoding='UTF-8'?>"
  21           + "<uniprot>"
  22           + "<entry dataset=\"TrEMBL\" created=\"2008-01-15\" modified=\"2015-03-04\" version=\"38\">"
  23           + "<accession>A9CKP4</accession>"
  24           + "<accession>A9CKP5</accession>"
  25           + "<name>A9CKP4_AGRT5</name>"
  26           + "<name>A9CKP4_AGRT6</name>"
  27           + "<protein><recommendedName><fullName>Mitogen-activated protein kinase 13</fullName><fullName>Henry</fullName></recommendedName></protein>"
  28           + "<dbReference type=\"PDB\" id=\"2FSQ\"><property type=\"method\" value=\"X-ray\"/><property type=\"resolution\" value=\"1.40\"/></dbReference>"
  29           + "<dbReference type=\"PDBsum\" id=\"2FSR\"/>"
  30           + "<feature type=\"signal peptide\" evidence=\"7\"><location><begin position=\"1\"/><end position=\"18\"/></location></feature>"
  31           + "<feature type=\"propeptide\" description=\"Activation peptide\" id=\"PRO_0000027399\" evidence=\"9 16 17 18\"><location><begin position=\"19\"/><end position=\"20\"/></location></feature>"
  32           + "<feature type=\"chain\" description=\"Granzyme B\" id=\"PRO_0000027400\"><location><begin position=\"21\"/><end position=\"247\"/></location></feature>"
  33           + "<sequence length=\"10\" mass=\"27410\" checksum=\"8CB760AACF88FE6C\" modified=\"2008-01-15\" version=\"1\">MHAPL VSKDL</sequence></entry>"
  34           + "</uniprot>";
  35
  36   /**
  37    * Test the method that unmarshals XML to a Uniprot model
  38    */
  39   @Test
  40   public void testGetUniprotEntries()
  41   {
  42     Uniprot u = new Uniprot();
  43     Reader reader = new StringReader(UNIPROT_XML);
  44     Vector<UniprotEntry> entries = u.getUniprotEntries(reader);
  45     assertEquals(1, entries.size());
  46     UniprotEntry entry = entries.get(0);
  47     assertEquals(2, entry.getName().size());
  48     assertEquals("A9CKP4_AGRT5", entry.getName().get(0));
  49     assertEquals("A9CKP4_AGRT6", entry.getName().get(1));
  50     assertEquals(2, entry.getAccession().size());
  51     assertEquals("A9CKP4", entry.getAccession().get(0));
  52     assertEquals("A9CKP5", entry.getAccession().get(1));
  53
  54     /*
  55      * UniprotSequence drops any space characters
  56      */
  57     assertEquals("MHAPLVSKDL", entry.getUniprotSequence()
  58             .getContent());
  59
  60     assertEquals(2, entry.getProtein().getName().size());
  61     assertEquals("Mitogen-activated protein kinase 13", entry.getProtein()
  62             .getName().get(0));
  63     assertEquals("Henry", entry.getProtein().getName().get(1));
  64
  65     /*
  66      * Check sequence features
  67      */
  68     Vector<SequenceFeature> features = entry.getFeature();
  69     assertEquals(3, features.size());
  70     SequenceFeature sf = features.get(0);
  71     assertEquals("signal peptide", sf.getType());
  72     assertNull(sf.getDescription());
  73     assertNull(sf.getStatus());
  74     assertEquals(1, sf.getPosition()); // wrong - Castor bug??
  75     assertEquals(1, sf.getBegin());
  76     assertEquals(18, sf.getEnd());
  77     sf = features.get(1);
  78     assertEquals("propeptide", sf.getType());
  79     assertEquals("Activation peptide", sf.getDescription());
  80     assertEquals(19, sf.getPosition()); // wrong - Castor bug??
  81     assertEquals(19, sf.getBegin());
  82     assertEquals(20, sf.getEnd());
  83     sf = features.get(2);
  84     assertEquals("chain", sf.getType());
  85     assertEquals("Granzyme B", sf.getDescription());
  86     assertEquals(21, sf.getPosition()); // wrong - Castor bug??
  87     assertEquals(21, sf.getBegin());
  88     assertEquals(247, sf.getEnd());
  89
  90     /*
  91      * Check cross-references
  92      */
  93     Vector<PDBEntry> xrefs = entry.getDbReference();
  94     assertEquals(2, xrefs.size());
  95
  96     PDBEntry xref = xrefs.get(0);
  97     assertEquals("2FSQ", xref.getId());
  98     assertEquals("PDB", xref.getType());
  99     assertEquals(2, xref.getProperty().size());
 100     assertEquals("X-ray", xref.getProperty().get("method"));
 101     assertEquals("1.40", xref.getProperty().get("resolution"));
 102
 103     xref = xrefs.get(1);
 104     assertEquals("2FSR", xref.getId());
 105     assertEquals("PDBsum", xref.getType());
 106     assertNull(xref.getProperty());
 107   }
 108
 109   /**
 110    * Test the method that formats the sequence name in Fasta style
 111    */
 112   @Test
 113   public void testConstructSequenceFastaHeader()
 114   {
 115     Uniprot u = new Uniprot();
 116     Reader reader = new StringReader(UNIPROT_XML);
 117     Vector<UniprotEntry> entries = u.getUniprotEntries(reader);
 118     UniprotEntry entry = entries.get(0);
 119
 120     // source + accession ids + names + protein names
 121     String expectedName = ">UniProt/Swiss-Prot|A9CKP4|A9CKP5|A9CKP4_AGRT5|A9CKP4_AGRT6 Mitogen-activated protein kinase 13 Henry";
 122     assertEquals(expectedName, Uniprot.constructSequenceFastaHeader(entry)
 123             .toString());
 124   }
 125
 126   @Test
 127   public void testuniref90_retrieve() throws Exception
 128   {
 129     AlignmentI rtn = new Uniprot().getSequenceRecords("UniRef90_V5TUP6");
 130     assertNotNull(rtn);
 131     assertEquals(rtn.getHeight(), 1);
 132   }
 133 }