/*
* 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.assertNotNull;
import static org.testng.AssertJUnit.assertNull;
import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.fail;
import java.io.File;
import java.io.IOException;
import java.net.MalformedURLException;
import java.util.Arrays;
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.Sequence.DBModList;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.datamodel.features.SequenceFeatures;
import jalview.util.MapList;
public class EmblFlatFileTest
{
@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.embl.txt");
FileParse fp = new FileParse(dataFile, DataSourceType.FILE);
EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
List seqs = parser.getSeqs();
assertEquals(seqs.size(), 1);
SequenceI seq = seqs.get(0);
assertEquals(seq.getName(), "EmblTest|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(), "EmblTest");
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(), "EmblTest");
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(), "EmblTest");
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(), "EmblTest");
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");
/*
* Verify DBRefs, whether declared in the file or added by Jalview.
* There are 4 'direct' (DR) dbrefs, and numerous CDS /db_xref entries
* (some e.g. INTERPRO are duplicates). Jalview adds a dbref to 'self'.
* Sample a few here. Note DBRefEntry constructor capitalises source.
*/
List dbrefs = seq.getDBRefs();
assertEquals(dbrefs.size(), 32);
// xref to 'self':
DBRefEntry selfRef = new DBRefEntry("EMBLTEST", "1", "J03321");
int[] range = new int[] { 1, seq.getLength() };
selfRef.setMap(new Mapping(null, range, range, 1, 1));
assertTrue(dbrefs.contains(selfRef));
// 1st DR line; note trailing period is removed
assertTrue(dbrefs.contains(new DBRefEntry("MD5", "0",
"d4c4942a634e3df4995fd5ac75c26a61")));
// the 4th DR line:
assertTrue(
dbrefs.contains(new DBRefEntry("EUROPEPMC", "0", "PMC87941")));
// from the first CDS feature
assertTrue(dbrefs.contains(new DBRefEntry("GOA", "0", "P0CE19")));
// from the last CDS feature
assertTrue(
dbrefs.contains(new DBRefEntry("INTERPRO", "0", "IPR005350")));
/*
* verify mappings to, and sequences for, UNIPROT proteins
*/
int uniprotCount = 0;
List ranges;
for (DBRefEntry dbref : dbrefs)
{
if ("UNIPROT".equals(dbref.getSource()))
{
uniprotCount++;
Mapping mapping = dbref.getMap();
assertNotNull(mapping);
MapList map = mapping.getMap();
String mappedToName = mapping.getTo().getName();
if ("UNIPROT|P0CE16".equals(mappedToName))
{
assertEquals((ranges = map.getFromRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1579);
assertEquals(ranges.get(0)[1], 2931); // excludes stop 2934
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 451);
// CDS /product carries over as protein product description
assertEquals(mapping.getTo().getDescription(),
"hypothetical protein");
}
else if ("UNIPROT|P0CE17".equals(mappedToName))
{
assertEquals((ranges = map.getFromRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 2928);
assertEquals(ranges.get(0)[1], 3989); // excludes stop 3992
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 354);
}
else if ("UNIPROT|P0CE18".equals(mappedToName))
{
assertEquals((ranges = map.getFromRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 4054);
assertEquals(ranges.get(0)[1], 4845); // excludes stop 4848
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 264);
}
else if ("UNIPROT|P0CE19".equals(mappedToName))
{
// join(7022..7502,1..437)
assertEquals((ranges = map.getFromRanges()).size(), 2);
assertEquals(ranges.get(0)[0], 7022);
assertEquals(ranges.get(0)[1], 7502);
assertEquals(ranges.get(1)[0], 1);
assertEquals(ranges.get(1)[1], 434); // excludes stop at 437
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 305);
}
else if ("UNIPROT|P0CE20".equals(mappedToName))
{
// complement(488..1480)
assertEquals((ranges = map.getFromRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1480);
assertEquals(ranges.get(0)[1], 491); // // excludes stop at 488
assertEquals((ranges = map.getToRanges()).size(), 1);
assertEquals(ranges.get(0)[0], 1);
assertEquals(ranges.get(0)[1], 330);
}
else if (!"UNIPROT|P0CE23".equals(mappedToName)
&& !"UNIPROT|P10559".equals(mappedToName)
&& !"UNIPROT|P10560".equals(mappedToName))
{
fail("Unexpected UNIPROT dbref to " + mappedToName);
}
}
}
assertEquals(uniprotCount, 8);
}
/**
* 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 testParseToRNA() throws MalformedURLException, IOException
{
File dataFile = new File("test/jalview/io/J03321_rna.embl.txt");
FileParse fp = new FileParse(dataFile, DataSourceType.FILE);
EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
List seqs = parser.getSeqs();
assertTrue(seqs.get(0).getSequenceAsString().indexOf("u") > -1);
}
@Test(groups = "Functional")
public void testParse_codonStartNot1()
{
// TODO verify CDS-to-protein mapping for CDS with /codon_start=2
// example: https://www.ebi.ac.uk/ena/browser/api/embl/EU498516
}
/**
* Test for the case that the EMBL CDS has no UNIPROT xref. In this case
* Jalview should synthesize an xref to EMBLCDSPROTEIN in the hope this will
* allow Get Cross-References.
*
* @throws IOException
*/
@Test(groups = "Functional")
public void testParse_noUniprotXref() throws IOException
{
// MN908947 cut down to 40BP, one CDS, length 5 peptide for test purposes
// plus an additional (invented) test case:
// - multi-line /product qualifier including escaped quotes
String data = "ID MN908947; SV 3; linear; genomic RNA; STD; VRL; 20 BP.\n"
+ "DE Severe acute respiratory syndrome coronavirus 2 isolate Wuhan-Hu-1,\n"
+ "FT CDS 3..17\n"
+ "FT /protein_id=\"QHD43415.1\"\n"
+ "FT /product=\"orf1ab polyprotein\n"
+ "FT \"\"foobar\"\" \"\n"
+ "FT /translation=\"MRKLD\n"
+ "SQ Sequence 7496 BP; 2450 A; 1290 C; 1434 G; 2322 T; 0 other;\n"
+ " ggatGcgtaa gttagacgaa attttgtctt tgcgcacaga 40\n";
FileParse fp = new FileParse(data, DataSourceType.PASTE);
EmblFlatFile parser = new EmblFlatFile(fp, "EmblTest");
List seqs = parser.getSeqs();
assertEquals(seqs.size(), 1);
SequenceI seq = seqs.get(0);
DBModList dbrefs = seq.getDBRefs();
/*
* dna should have dbref to itself, and to inferred EMBLCDSPROTEIN:QHD43415.1
*/
assertEquals(dbrefs.size(), 2);
// dbref to self
DBRefEntry dbref = dbrefs.get(0);
assertEquals(dbref.getSource(), "EMBLTEST");
assertEquals(dbref.getAccessionId(), "MN908947");
Mapping mapping = dbref.getMap();
assertNull(mapping.getTo());
MapList map = mapping.getMap();
assertEquals(map.getFromLowest(), 1);
assertEquals(map.getFromHighest(), 40);
assertEquals(map.getToLowest(), 1);
assertEquals(map.getToHighest(), 40);
assertEquals(map.getFromRatio(), 1);
assertEquals(map.getToRatio(), 1);
// dbref to inferred EMBLCDSPROTEIN:
dbref = dbrefs.get(1);
assertEquals(dbref.getSource(), "EMBLCDSPROTEIN");
assertEquals(dbref.getAccessionId(), "QHD43415.1");
mapping = dbref.getMap();
SequenceI mapTo = mapping.getTo();
assertEquals(mapTo.getName(), "QHD43415.1");
// the /product qualifier transfers to protein product description
assertEquals(mapTo.getDescription(), "orf1ab polyprotein \"foobar\"");
assertEquals(mapTo.getSequenceAsString(), "MRKLD");
map = mapping.getMap();
assertEquals(map.getFromLowest(), 3);
assertEquals(map.getFromHighest(), 17);
assertEquals(map.getToLowest(), 1);
assertEquals(map.getToHighest(), 5);
assertEquals(map.getFromRatio(), 3);
assertEquals(map.getToRatio(), 1);
}
@Test(groups = "Functional")
public void testAdjustForProteinLength()
{
int[] exons = new int[] { 11, 15, 21, 25, 31, 38 }; // 18 bp
// exact length match:
assertSame(exons, EmblFlatFile.adjustForProteinLength(6, exons));
// patch from JAL-3725 in EmblXmlSource propagated to Flatfile
// match if we assume exons include stop codon not in protein:
int[] truncated = EmblFlatFile.adjustForProteinLength(5, exons);
assertEquals(Arrays.toString(truncated), "[11, 15, 21, 25, 31, 35]");
// truncate last exon by 6bp
truncated = EmblFlatFile.adjustForProteinLength(4, exons);
assertEquals(Arrays.toString(truncated), "[11, 15, 21, 25, 31, 32]");
// remove last exon and truncate preceding by 1bp (so 3bp in total)
truncated = EmblFlatFile.adjustForProteinLength(3, exons);
assertEquals(Arrays.toString(truncated), "[11, 15, 21, 24]");
// exact removal of exon case:
exons = new int[] { 11, 15, 21, 27, 33, 38 }; // 18 bp
truncated = EmblFlatFile.adjustForProteinLength(4, exons);
assertEquals(Arrays.toString(truncated), "[11, 15, 21, 27]");
// what if exons are too short for protein?
truncated = EmblFlatFile.adjustForProteinLength(7, exons);
assertSame(exons, truncated);
}
@Test(groups = "Functional")
public void testRemoveQuotes()
{
assertNull(EmblFlatFile.removeQuotes(null));
assertEquals(EmblFlatFile.removeQuotes("No quotes here"),
"No quotes here");
assertEquals(EmblFlatFile.removeQuotes("\"Enclosing quotes\""),
"Enclosing quotes");
assertEquals(
EmblFlatFile.removeQuotes("\"Escaped \"\"quotes\"\" example\""),
"Escaped \"quotes\" example");
}
}