test/jalview/ws/dbsources/UniprotTest.java

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