/*
* Jalview - A Sequence Alignment Editor and Viewer ($$Version-Rel$$)
* Copyright (C) $$Year-Rel$$ The Jalview Authors
*
* This file is part of Jalview.
*
* Jalview is free software: you can redistribute it and/or
* modify it under the terms of the GNU General Public License
* as published by the Free Software Foundation, either version 3
* of the License, or (at your option) any later version.
*
* Jalview is distributed in the hope that it will be useful, but
* WITHOUT ANY WARRANTY; without even the implied warranty
* of MERCHANTABILITY or FITNESS FOR A PARTICULAR
* PURPOSE. See the GNU General Public License for more details.
*
* You should have received a copy of the GNU General Public License
* along with Jalview. If not, see .
* The Jalview Authors are detailed in the 'AUTHORS' file.
*/
package jalview.io;
import static org.testng.Assert.assertEquals;
import static org.testng.Assert.assertTrue;
import static org.testng.AssertJUnit.assertNull;
import java.io.File;
import java.io.IOException;
import java.net.MalformedURLException;
import java.util.List;
import java.util.Set;
import org.testng.annotations.BeforeClass;
import org.testng.annotations.Test;
import jalview.bin.Console;
import jalview.datamodel.DBRefEntry;
import jalview.datamodel.Mapping;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.SequenceFeatures;
import jalview.util.MapList;
public class GenBankFileTest
{
@BeforeClass(alwaysRun = true)
public void setUp()
{
Console.initLogger();
}
/**
* A fairly tough test, using J03321 (circular DNA), which has 8 CDS features,
* one of them reverse strand
*
* @throws MalformedURLException
* @throws IOException
*/
@Test(groups = "Functional")
public void testParse() throws MalformedURLException, IOException
{
File dataFile = new File("test/jalview/io/J03321.gb");
FileParse fp = new FileParse(dataFile.getAbsolutePath(),
DataSourceType.FILE);
EMBLLikeFlatFile parser = new GenBankFile(fp, "GenBankTest");
List seqs = parser.getSeqs();
assertEquals(seqs.size(), 1);
SequenceI seq = seqs.get(0);
assertEquals(seq.getName(), "GenBankTest|J03321");
assertEquals(seq.getLength(), 7502);
assertEquals(seq.getDescription(),
"Chlamydia trachomatis plasmid pCHL1, complete sequence");
/*
* should be 9 CDS features (one is a 'join' of two exons)
*/
Set featureTypes = seq.getFeatures().getFeatureTypes();
assertEquals(featureTypes.size(), 1);
assertTrue(featureTypes.contains("CDS"));
/*
* inspect some features (sorted just for convenience of test assertions)
*/
List features = seq.getFeatures()
.getAllFeatures("CDS");
SequenceFeatures.sortFeatures(features, true);
assertEquals(features.size(), 9);
SequenceFeature sf = features.get(0);
assertEquals(sf.getBegin(), 1);
assertEquals(sf.getEnd(), 437);
assertEquals(sf.getDescription(),
"Exon 2 for protein EMBLCDS:AAA91567.1");
assertEquals(sf.getFeatureGroup(), "GenBankTest");
assertEquals(sf.getEnaLocation(), "join(7022..7502,1..437)");
assertEquals(sf.getPhase(), "0");
assertEquals(sf.getStrand(), 1);
assertEquals(sf.getValue("note"), "pGP7-D");
// this is the second exon of circular CDS!
assertEquals(sf.getValue("exon number"), 2);
assertEquals(sf.getValue("product"), "hypothetical protein");
assertEquals(sf.getValue("transl_table"), "11");
sf = features.get(1);
assertEquals(sf.getBegin(), 488);
assertEquals(sf.getEnd(), 1480);
assertEquals(sf.getDescription(),
"Exon 1 for protein EMBLCDS:AAA91568.1");
assertEquals(sf.getFeatureGroup(), "GenBankTest");
assertEquals(sf.getEnaLocation(), "complement(488..1480)");
assertEquals(sf.getPhase(), "0");
assertEquals(sf.getStrand(), -1); // reverse strand!
assertEquals(sf.getValue("note"), "pGP8-D");
assertEquals(sf.getValue("exon number"), 1);
assertEquals(sf.getValue("product"), "hypothetical protein");
sf = features.get(7);
assertEquals(sf.getBegin(), 6045);
assertEquals(sf.getEnd(), 6788);
assertEquals(sf.getDescription(),
"Exon 1 for protein EMBLCDS:AAA91574.1");
assertEquals(sf.getFeatureGroup(), "GenBankTest");
assertEquals(sf.getEnaLocation(), "6045..6788");
assertEquals(sf.getPhase(), "0");
assertEquals(sf.getStrand(), 1);
assertEquals(sf.getValue("note"), "pGP6-D (gtg start codon)");
assertEquals(sf.getValue("exon number"), 1);
assertEquals(sf.getValue("product"), "hypothetical protein");
/*
* CDS at 7022-7502 is the first exon of the circular CDS
*/
sf = features.get(8);
assertEquals(sf.getBegin(), 7022);
assertEquals(sf.getEnd(), 7502);
assertEquals(sf.getDescription(),
"Exon 1 for protein EMBLCDS:AAA91567.1");
assertEquals(sf.getFeatureGroup(), "GenBankTest");
assertEquals(sf.getEnaLocation(), "join(7022..7502,1..437)");
assertEquals(sf.getPhase(), "0");
assertEquals(sf.getStrand(), 1);
assertEquals(sf.getValue("note"), "pGP7-D");
assertEquals(sf.getValue("exon number"), 1);
assertEquals(sf.getValue("product"), "hypothetical protein");
/*
* GenBank doesn't declare accession or CDS xrefs;
* dbrefs are added by Jalview for
* xref to self : 1
* protein products: 8
*/
List dbrefs = seq.getDBRefs();
assertEquals(dbrefs.size(), 9);
// xref to 'self':
DBRefEntry selfRef = new DBRefEntry("GENBANKTEST", "1", "J03321");
int[] range = new int[] { 1, seq.getLength() };
selfRef.setMap(new Mapping(null, range, range, 1, 1));
assertTrue(dbrefs.contains(selfRef));
/*
* dna should have dbref to itself, and to EMBLCDSPROTEIN
* for each /protein_id (synthesized as no UNIPROT xref)
*/
// TODO check if we should synthesize EMBLCDSPROTEIN dbrefs
DBRefEntry dbref = dbrefs.get(0);
assertEquals(dbref.getSource(), "GENBANKTEST");
assertEquals(dbref.getAccessionId(), "J03321");
Mapping mapping = dbref.getMap();
assertNull(mapping.getTo());
MapList map = mapping.getMap();
assertEquals(map.getFromLowest(), 1);
assertEquals(map.getFromHighest(), 7502);
assertEquals(map.getToLowest(), 1);
assertEquals(map.getToHighest(), 7502);
assertEquals(map.getFromRatio(), 1);
assertEquals(map.getToRatio(), 1);
// dbref to inferred EMBLCDSPROTEIN for first CDS
dbref = dbrefs.get(1);
assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
assertEquals(dbref.getAccessionId(), "AAA91567.1");
mapping = dbref.getMap();
SequenceI mapTo = mapping.getTo();
assertEquals(mapTo.getName(), "AAA91567.1");
// the /product qualifier transfers to protein product description
assertEquals(mapTo.getDescription(), "hypothetical protein");
String seqString = mapTo.getSequenceAsString();
assertEquals(seqString.length(), 305);
assertTrue(seqString.startsWith("MGSMAF"));
assertTrue(seqString.endsWith("QTPTIL"));
map = mapping.getMap();
assertEquals(map.getFromLowest(), 1);
assertEquals(map.getFromHighest(), 7502);
assertEquals(map.getToLowest(), 1);
assertEquals(map.getToHighest(), 305);
assertEquals(map.getFromRatio(), 3);
assertEquals(map.getToRatio(), 1);
// dbref to inferred EMBLCDSPROTEIN for last CDS
dbref = dbrefs.get(8);
assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
assertEquals(dbref.getAccessionId(), "AAA91574.1");
mapping = dbref.getMap();
mapTo = mapping.getTo();
assertEquals(mapTo.getName(), "AAA91574.1");
// the /product qualifier transfers to protein product description
assertEquals(mapTo.getDescription(), "hypothetical protein");
seqString = mapTo.getSequenceAsString();
assertEquals(seqString.length(), 247);
assertTrue(seqString.startsWith("MNKLK"));
assertTrue(seqString.endsWith("FKQKS"));
map = mapping.getMap();
assertEquals(map.getFromLowest(), 6045);
assertEquals(map.getFromHighest(), 6785); // excludes stop at 6788
assertEquals(map.getToLowest(), 1);
assertEquals(map.getToHighest(), 247);
assertEquals(map.getFromRatio(), 3);
assertEquals(map.getToRatio(), 1);
}
}