validation tests

test/uk/ac/sanger/artemis/io/ValidateFeatureTest.java

+package uk.ac.sanger.artemis.io;
+
+import static org.junit.Assert.assertEquals;
+import static org.junit.Assert.assertTrue;
+
+import java.io.IOException;
+import java.net.URL;
+import java.util.LinkedHashMap;
+import java.util.Map;
+
+import org.apache.log4j.Level;
+import org.junit.Test;
+
+import junit.framework.Assert;
+
+import uk.ac.sanger.artemis.EntryGroup;
+import uk.ac.sanger.artemis.Options;
+import uk.ac.sanger.artemis.SimpleEntryGroup;
+import uk.ac.sanger.artemis.components.EntryFileDialog;
+import uk.ac.sanger.artemis.components.genebuilder.GeneUtils;
+import uk.ac.sanger.artemis.io.DocumentEntryFactory;
+import uk.ac.sanger.artemis.io.Entry;
+import uk.ac.sanger.artemis.io.EntryInformationException;
+import uk.ac.sanger.artemis.io.FeatureVector;
+import uk.ac.sanger.artemis.io.GFFStreamFeature;
+import uk.ac.sanger.artemis.io.ValidateFeature;
+import uk.ac.sanger.artemis.util.Document;
+import uk.ac.sanger.artemis.util.DocumentFactory;
+import uk.ac.sanger.artemis.util.OutOfRangeException;
+import uk.ac.sanger.artemis.sequence.NoSequenceException;
+
+public class ValidateFeatureTest
+{
+  @Test
+  public void testGFF()
+  {
+    try 
+    {
+      final Entry entry = getEntry("/data/test.gff.gz");
+      final EntryGroup egrp = new SimpleEntryGroup();
+      egrp.add(new uk.ac.sanger.artemis.Entry(entry));
+      ValidateFeature validate = new ValidateFeature(egrp);
+      
+      final FeatureVector features = entry.getAllFeatures();
+
+      for(uk.ac.sanger.artemis.io.Feature f: features)
+      {
+        if(ValidateFeature.isGFF(f, null))
+        {
+          GFFStreamFeature gffFeature = (GFFStreamFeature)f;
+          String id = GeneUtils.getUniqueName(gffFeature);
+          
+          assertTrue("Boundary "+id,  ValidateFeature.isBoundaryOK(gffFeature) == 0);
+          assertTrue("Strand "+id,    ValidateFeature.isStrandOK(gffFeature));
+          assertTrue("CDS phase "+id, ValidateFeature.isCDSPhaseOK(gffFeature));
+          assertTrue("Attribute "+id, ValidateFeature.isAttributesOK(gffFeature).length() == 0);
+          assertTrue("ID check "+id, ValidateFeature.isIdPrefixConsistent(gffFeature));
+          assertTrue("Start_range check "+id, ValidateFeature.isPartialConsistent(gffFeature, "Start_range"));
+          assertTrue("End_range check "+id, ValidateFeature.isPartialConsistent(gffFeature, "End_range"));
+
+          if(ValidateFeature.isPartOfGene(gffFeature))
+            assertTrue("Gene model "+id, ValidateFeature.isCompleteGeneModelOK(gffFeature) == 0);
+        }
+
+        assertTrue("Stop codon", validate.hasValidStop(f));
+        assertTrue("Internal stop codon", !validate.isInternalStops(f));
+      }
+    }
+    catch(OutOfRangeException e)
+    {
+      Assert.fail(e.getMessage());
+    }
+    catch(NoSequenceException e)
+    {
+      Assert.fail(e.getMessage());
+    }
+  }
+  
+  /**
+   * Test the gene model boundary is consistent
+   */
+  @Test
+  public void testGFFBoundary()
+  {
+    final Entry entry = getEntry("/data/test_boundary.gff.gz");
+    final FeatureVector features = entry.getAllFeatures();
+
+    for(uk.ac.sanger.artemis.io.Feature f: features)
+    {
+      if(ValidateFeature.isGFF(f, null))
+      {
+        GFFStreamFeature gffFeature = (GFFStreamFeature)f;
+        String id = GeneUtils.getUniqueName(gffFeature);
+        if(id.equals("PF3D7_0200100"))
+          assertTrue("Boundary check: "+id, ValidateFeature.isBoundaryOK(gffFeature) != 0); // boundary not OK
+        else
+          assertTrue("Boundary check: "+id, ValidateFeature.isBoundaryOK(gffFeature) == 0); // boundary OK
+      }
+    }
+  }
+  
+  /**
+   * Test the gene model strand is consistent
+   */
+  @Test
+  public void testGFFStrand()
+  {
+    final Entry entry = getEntry("/data/test_boundary.gff.gz");
+    final FeatureVector features = entry.getAllFeatures();
+
+    for(uk.ac.sanger.artemis.io.Feature f: features)
+    {
+      if(ValidateFeature.isGFF(f, null))
+      {
+        GFFStreamFeature gffFeature = (GFFStreamFeature)f;
+        String id = GeneUtils.getUniqueName(gffFeature);
+        if(id.equals("PF3D7_0200300"))
+          assertTrue("Strand check: "+id, !ValidateFeature.isStrandOK(gffFeature)); // strand not ok
+        else
+          assertTrue("Strand check: "+id, ValidateFeature.isStrandOK(gffFeature));  // strand ok
+      }
+    }
+  }
+  
+  /**
+   * Test the CDS has a phase
+   */
+  @Test
+  public void testGFFPhase()
+  {
+    final Entry entry = getEntry("/data/test_boundary.gff.gz");
+    final FeatureVector features = entry.getAllFeatures();
+
+    for(uk.ac.sanger.artemis.io.Feature f: features)
+    {
+      if(ValidateFeature.isGFF(f, null))
+      {
+        GFFStreamFeature gffFeature = (GFFStreamFeature)f;
+        String id = GeneUtils.getUniqueName(gffFeature);
+        if(id.equals("PF3D7_0200200.1:exon{2,1}"))
+          assertTrue("CDS phase check: "+id, !ValidateFeature.isCDSPhaseOK(gffFeature)); // phase not ok
+        else
+          assertTrue("CDS phase check: "+id, ValidateFeature.isCDSPhaseOK(gffFeature));  // phase ok
+      }
+    }
+  }
+  
+  /**
+   * Test the gene models are complete
+   */
+  @Test
+  public void testGFFCompleteGeneModel()
+  {
+    final Entry entry = getEntry("/data/test_boundary.gff.gz");
+    final FeatureVector features = entry.getAllFeatures();
+
+    for(uk.ac.sanger.artemis.io.Feature f: features)
+    {
+      if(ValidateFeature.isGFF(f, null))
+      {
+        GFFStreamFeature gffFeature = (GFFStreamFeature)f;
+        if(ValidateFeature.isPartOfGene(gffFeature))
+        {
+          String id = GeneUtils.getUniqueName(gffFeature);
+          if(id.startsWith("PF3D7_0200500")) 
+            assertTrue("Complete gene model check: "+id,   // gene model missing mRNA
+                ValidateFeature.isCompleteGeneModelOK(gffFeature) != 0);
+          else
+            assertTrue("Complete gene model check: "+id,   // gene model complete
+                ValidateFeature.isCompleteGeneModelOK(gffFeature) == 0);
+        }
+      }
+    }
+  }
+  
+  
+  /**
+   * Test if the ID GFF3 attribute prefix is consistent within a gene model
+   */
+  @Test
+  public void testGFFId()
+  {
+    final Entry entry = getEntry("/data/test_boundary.gff.gz");
+    final FeatureVector features = entry.getAllFeatures();
+
+    for(uk.ac.sanger.artemis.io.Feature f: features)
+    {
+      if(ValidateFeature.isGFF(f, null))
+      {
+        GFFStreamFeature gffFeature = (GFFStreamFeature)f;
+        if(ValidateFeature.isPartOfGene(gffFeature))
+        {
+          String id = GeneUtils.getUniqueName(gffFeature);
+          assertTrue("Complete gene model check: "+id,
+              ValidateFeature.isIdPrefixConsistent(gffFeature));
+        }
+      }
+    }
+  }
+  
+  
+  /**
+   * Test if the Start_range and End_range are constistent within a gene model
+   */
+  @Test
+  public void testGFFPartials()
+  {
+    final Entry entry = getEntry("/data/test_boundary.gff.gz");
+    final FeatureVector features = entry.getAllFeatures();
+
+    for(uk.ac.sanger.artemis.io.Feature f: features)
+    {
+      if(ValidateFeature.isGFF(f, null))
+      {
+        GFFStreamFeature gffFeature = (GFFStreamFeature)f;
+        if(ValidateFeature.isPartOfGene(gffFeature))
+        {
+          String id = GeneUtils.getUniqueName(gffFeature);
+          assertTrue("Start_range check: "+id,
+              ValidateFeature.isPartialConsistent(gffFeature, "Start_range"));
+          assertTrue("End_range check: "+id,
+              ValidateFeature.isPartialConsistent(gffFeature, "End_range"));
+        }
+      }
+    }
+  }
+  
+  
+  /**
+   * Test if the Start_range and End_range are constistent within a gene model
+   */
+  @Test
+  public void testGFFAttributes()
+  {
+    final Entry entry = getEntry("/data/test_boundary.gff.gz");
+    final FeatureVector features = entry.getAllFeatures();
+
+    for(uk.ac.sanger.artemis.io.Feature f: features)
+    {
+      if(ValidateFeature.isGFF(f, null))
+      {
+        GFFStreamFeature gffFeature = (GFFStreamFeature)f;
+        if(ValidateFeature.isPartOfGene(gffFeature))
+        {
+          String id = GeneUtils.getUniqueName(gffFeature);
+          assertTrue("Attributes : "+id,
+              ValidateFeature.isAttributesOK(gffFeature).length() == 0);
+        }
+      }
+    }
+  }
+  
+  
+  /**
+   * Test stop codons for genes
+   */
+  @Test
+  public void testGFFValidStop()
+  {
+    try
+    {
+      final Entry entry = getEntry("/data/test_boundary.gff.gz");
+      final FeatureVector features = entry.getAllFeatures();
+      final EntryGroup egrp = new SimpleEntryGroup();
+      egrp.add(new uk.ac.sanger.artemis.Entry(entry));
+      ValidateFeature validate = new ValidateFeature(egrp);
+
+      for (uk.ac.sanger.artemis.io.Feature f : features)
+      {
+        GFFStreamFeature gffFeature = (GFFStreamFeature)f;
+        String id = GeneUtils.getUniqueName(gffFeature);
+        if( (id.startsWith("PF3D7_0200100") || id.startsWith("PF3D7_0200500.1:exon:2")) && 
+            f.getKey().getKeyString().equals("CDS"))
+          assertTrue("Stop codon "+id, !validate.hasValidStop(f)); // not valid
+        else
+          assertTrue("Stop codon "+id, validate.hasValidStop(f));
+      }
+    }
+    catch (OutOfRangeException e)
+    {
+      Assert.fail(e.getMessage());
+    }
+    catch (NoSequenceException e)
+    {
+      Assert.fail(e.getMessage());
+    }
+  }
+
+  /**
+   * Test for internal stop codons
+   */
+  @Test
+  public void testGFFInternalStop()
+  {
+    try
+    {
+      final Entry entry = getEntry("/data/test_boundary.gff.gz");
+      final FeatureVector features = entry.getAllFeatures();
+      final EntryGroup egrp = new SimpleEntryGroup();
+      egrp.add(new uk.ac.sanger.artemis.Entry(entry));
+      ValidateFeature validate = new ValidateFeature(egrp);
+
+      for (uk.ac.sanger.artemis.io.Feature f : features)
+      {
+        GFFStreamFeature gffFeature = (GFFStreamFeature)f;
+        String id = GeneUtils.getUniqueName(gffFeature);
+        assertTrue("Internal stop codon "+id, !validate.isInternalStops(f));
+      }
+    }
+    catch (OutOfRangeException e)
+    {
+      Assert.fail(e.getMessage());
+    }
+    catch (NoSequenceException e)
+    {
+      Assert.fail(e.getMessage());
+    }
+  }
+  
+  
+  private Entry getEntry(final String gff)
+  {
+    try
+    {
+      URL gffFile = ValidateFeatureTest.class.getResource(gff);
+      final Document doc = DocumentFactory.makeDocument(gffFile.getFile());
+      return DocumentEntryFactory.makeDocumentEntry(
+          Options.getArtemisEntryInformation(),doc,null);
+    }
+    catch(EntryInformationException e) 
+    {
+      Assert.fail(e.getMessage());
+    }
+    catch(IOException e) 
+    {
+      Assert.fail(e.getMessage());
+    }
+    return null;
+  }
+}
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