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/*
* BioJava development code
*
* This code may be freely distributed and modified under the
* terms of the GNU Lesser General Public Licence. This should
* be distributed with the code. If you do not have a copy,
* see:
*
* http://www.gnu.org/copyleft/lesser.html
*
* Copyright for this code is held jointly by the individual
* authors. These should be listed in @author doc comments.
*
* For more information on the BioJava project and its aims,
* or to join the biojava-l mailing list, visit the home page
* at:
*
* http://www.biojava.org/
*
*/
package org.biojava.nbio.core.sequence.loader;
import org.biojava.nbio.core.exceptions.CompoundNotFoundException;
import org.biojava.nbio.core.sequence.ProteinSequence;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompound;
import org.biojava.nbio.core.sequence.compound.AminoAcidCompoundSet;
import org.biojava.nbio.core.sequence.features.FeatureInterface;
import org.biojava.nbio.core.sequence.template.AbstractSequence;
import org.junit.Assert;
import org.junit.Test;
import org.junit.runner.RunWith;
import org.junit.runners.Parameterized;
import org.slf4j.Logger;
import org.slf4j.LoggerFactory;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
import java.util.Collection;
import org.biojava.nbio.core.sequence.features.AbstractFeature;
import org.biojava.nbio.core.sequence.features.Qualifier;
/**
* Testing example for issue #834
*
* @author Jacek Grzebyta
* @author Paolo Pavan
* @see InfoTask
*/
@RunWith(Parameterized.class)
public class GenbankProxySequenceReaderTest {
private String gi;
private final static Logger logger = LoggerFactory.getLogger(GenbankProxySequenceReaderTest.class);
public GenbankProxySequenceReaderTest(String gi) {
this.gi = gi;
}
@Parameterized.Parameters
public static Collection<String[]> getExamples() {
String[][] out = new String[][]{
{"399235158"},
{"7525057"},
{"379015144"},
{"381353147"},
{"381353148"},
{"152970917"},
{"381353149"},
{"254839678"}
};
return Arrays.asList(out);
}
@Test
public void testFeatures() throws IOException, InterruptedException, CompoundNotFoundException {
logger.info("run test for protein: {}", gi);
GenbankProxySequenceReader<AminoAcidCompound> genbankReader
= new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"),
this.gi,
AminoAcidCompoundSet.getAminoAcidCompoundSet());
// why only tests on protein sequences?
ProteinSequence seq = new ProteinSequence(genbankReader);
Assert.assertNotNull("protein sequence is null", seq);
/*
parse description from header. There is no separate interface/abstract class for method getHeader()
so it should be done here (manualy).
*/
genbankReader.getHeaderParser().parseHeader(genbankReader.getHeader(), seq);
// test description
Assert.assertTrue(seq.getDescription() != null);
// test accession Id
logger.info("accession id: {}", seq.getAccession().getID());
Assert.assertNotNull(seq.getAccession().getID());
// test GID number
if( seq.getAccession().getIdentifier() != null) { // GI: in header now optional. See #596
Assert.assertEquals(gi, seq.getAccession().getIdentifier());
logger.info("found identifier '{}'", seq.getAccession().getIdentifier());
}
// test taxonomy id
logger.info("taxonomy id: {}", seq.getTaxonomy().getID());
Assert.assertNotNull(seq.getTaxonomy().getID());
Assert.assertNotNull(Integer.decode(seq.getTaxonomy().getID().split(":")[1]));
// test taxonomy name
String taxonName = seq.getFeaturesByType("source").get(0).getQualifiers().get("organism").get(0).getValue();
logger.info("taxonomy name '{}'", taxonName);
Assert.assertNotNull(taxonName);
if (seq.getFeaturesByType("CDS").size() > 0) {
FeatureInterface<AbstractSequence<AminoAcidCompound>, AminoAcidCompound> CDS = seq.getFeaturesByType("CDS").get(0);
logger.info("CDS: {}", CDS);
String codedBy = CDS.getQualifiers().get("coded_by").get(0).getValue();
Assert.assertNotNull(codedBy);
Assert.assertTrue(!codedBy.isEmpty());
logger.info("\t\tcoded_by: {}", codedBy);
}
}
@Test
public void testProteinSequenceFactoring() throws Exception {
logger.info("create protein sequence test for target {}", gi);
GenbankProxySequenceReader<AminoAcidCompound> genbankReader
= new GenbankProxySequenceReader<AminoAcidCompound>(System.getProperty("java.io.tmpdir"),
this.gi,
AminoAcidCompoundSet.getAminoAcidCompoundSet());
ProteinSequence seq = new ProteinSequence(genbankReader);
// if target protein contain CDS/coded_by than it should contain parent nucleotide seq
ArrayList<AbstractFeature> CDSs = genbankReader.getFeatures().get("CDS");
if (CDSs != null) {
if (CDSs.size() == 1) {
ArrayList<Qualifier> qualifiers = (ArrayList)CDSs.get(0).getQualifiers().get("coded_by");
Qualifier codedBy = qualifiers.get(0);
if (codedBy != null) {
AbstractSequence<?> parentSeq = seq.getParentSequence();
Assert.assertNotNull(parentSeq);
/*
Sometimes protein might have many 'parents' with different accessions
so accession is not set.
That test is always failed
*/
//Assert.assertTrue(parentSeq.getAccession());
Assert.assertTrue(!parentSeq.getSequenceAsString().isEmpty());
}
}
} else {
logger.info("target {} has no CDS", gi);
}
}
}
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