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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;
}
}