import static org.testng.AssertJUnit.assertSame;
import static org.testng.AssertJUnit.assertTrue;
+import jalview.analysis.AlignmentUtils.DnaVariant;
import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.Alignment;
import jalview.datamodel.AlignmentAnnotation;
import jalview.datamodel.SearchResults;
import jalview.datamodel.SearchResults.Match;
import jalview.datamodel.Sequence;
+import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.AppletFormatAdapter;
+import jalview.io.DataSourceType;
+import jalview.io.FileFormat;
+import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
import jalview.util.MapList;
import jalview.util.MappingUtils;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
-import java.util.HashSet;
import java.util.Iterator;
+import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
-import java.util.Set;
+import java.util.TreeMap;
import org.testng.annotations.Test;
public class AlignmentUtilsTests
{
- // @formatter:off
- private static final String TEST_DATA =
- "# STOCKHOLM 1.0\n" +
- "#=GS D.melanogaster.1 AC AY119185.1/838-902\n" +
- "#=GS D.melanogaster.2 AC AC092237.1/57223-57161\n" +
- "#=GS D.melanogaster.3 AC AY060611.1/560-627\n" +
- "D.melanogaster.1 G.AGCC.CU...AUGAUCGA\n" +
- "#=GR D.melanogaster.1 SS ................((((\n" +
- "D.melanogaster.2 C.AUUCAACU.UAUGAGGAU\n" +
- "#=GR D.melanogaster.2 SS ................((((\n" +
- "D.melanogaster.3 G.UGGCGCU..UAUGACGCA\n" +
- "#=GR D.melanogaster.3 SS (.(((...(....(((((((\n" +
- "//";
-
- private static final String AA_SEQS_1 =
- ">Seq1Name\n" +
- "K-QY--L\n" +
- ">Seq2Name\n" +
- "-R-FP-W-\n";
-
- private static final String CDNA_SEQS_1 =
- ">Seq1Name\n" +
- "AC-GG--CUC-CAA-CT\n" +
- ">Seq2Name\n" +
- "-CG-TTA--ACG---AAGT\n";
-
- private static final String CDNA_SEQS_2 =
- ">Seq1Name\n" +
- "GCTCGUCGTACT\n" +
- ">Seq2Name\n" +
- "GGGTCAGGCAGT\n";
- // @formatter:on
-
- // public static Sequence ts=new
- // Sequence("short","ASDASDASDASDASDASDASDASDASDASDASDASDASD");
public static Sequence ts = new Sequence("short",
"ABCDEFGHIJKLMNOPQRSTUVWXYZabcdefghijklm");
SequenceI s1 = ts.deriveSequence().getSubSequence(i, i + 7);
al.addSequence(s1);
}
- System.out.println(new AppletFormatAdapter().formatSequences("Clustal",
+ System.out.println(new AppletFormatAdapter().formatSequences(
+ FileFormat.Clustal,
al, true));
for (int flnk = -1; flnk < 25; flnk++)
{
AlignmentI exp = AlignmentUtils.expandContext(al, flnk);
System.out.println("\nFlank size: " + flnk);
System.out.println(new AppletFormatAdapter().formatSequences(
- "Clustal", exp, true));
+ FileFormat.Clustal, exp, true));
if (flnk == -1)
{
/*
{
final String data = ">Seq1Name\nKQYL\n" + ">Seq2Name\nRFPW\n"
+ ">Seq1Name\nABCD\n";
- AlignmentI al = loadAlignment(data, "FASTA");
+ AlignmentI al = loadAlignment(data, FileFormat.Fasta);
Map<String, List<SequenceI>> map = AlignmentUtils
.getSequencesByName(al);
assertEquals(2, map.keySet().size());
* @return
* @throws IOException
*/
- protected AlignmentI loadAlignment(final String data, String format)
+ protected AlignmentI loadAlignment(final String data, FileFormatI format)
throws IOException
{
AlignmentI a = new FormatAdapter().readFile(data,
- AppletFormatAdapter.PASTE, format);
+ DataSourceType.PASTE, format);
a.setDataset(null);
return a;
}
}
/**
- * Test for the method that generates an aligned translated sequence from one
- * mapping.
- */
- @Test(groups = { "Functional" })
- public void testGetAlignedTranslation_dnaLikeProtein()
- {
- // dna alignment will be replaced
- SequenceI dna = new Sequence("Seq1", "T-G-CC-A--T-TAC-CAG-");
- dna.createDatasetSequence();
- // protein alignment will be 'applied' to dna
- SequenceI protein = new Sequence("Seq1", "-CH-Y--Q-");
- protein.createDatasetSequence();
- MapList map = new MapList(new int[] { 1, 12 }, new int[] { 1, 4 }, 3, 1);
- AlignedCodonFrame acf = new AlignedCodonFrame();
- acf.addMap(dna.getDatasetSequence(), protein.getDatasetSequence(), map);
-
- final SequenceI aligned = AlignmentUtils.getAlignedTranslation(protein,
- '-', acf);
- assertEquals("---TGCCAT---TAC------CAG---",
- aligned.getSequenceAsString());
- assertSame(aligned.getDatasetSequence(), dna.getDatasetSequence());
- }
-
- /**
* Test the method that realigns protein to match mapped codon alignment.
*/
@Test(groups = { "Functional" })
@Test(groups = { "Functional" })
public void testTranslatesAs()
{
+ // null arguments check
+ assertFalse(AlignmentUtils.translatesAs(null, 0, null));
+ assertFalse(AlignmentUtils.translatesAs(new char[] { 't' }, 0, null));
+ assertFalse(AlignmentUtils.translatesAs(null, 0, new char[] { 'a' }));
+
+ // straight translation
assertTrue(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(), 0,
"FPKG".toCharArray()));
- // with start codon (not in protein)
+ // with extra start codon (not in protein)
assertTrue(AlignmentUtils.translatesAs("atgtttcccaaaggg".toCharArray(),
3, "FPKG".toCharArray()));
// with stop codon1 (not in protein)
assertTrue(AlignmentUtils.translatesAs(
"atgtttcccaaagggtga".toCharArray(), 3, "FPKG".toCharArray()));
- // with embedded stop codon
+ // with embedded stop codons
assertTrue(AlignmentUtils.translatesAs(
"atgtttTAGcccaaaTAAgggtga".toCharArray(), 3,
"F*PK*G".toCharArray()));
// wrong protein
assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
0, "FPMG".toCharArray()));
+
+ // truncated dna
+ assertFalse(AlignmentUtils.translatesAs("tttcccaaagg".toCharArray(), 0,
+ "FPKG".toCharArray()));
+
+ // truncated protein
+ assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
+ 0, "FPK".toCharArray()));
+
+ // overlong dna (doesn't end in stop codon)
+ assertFalse(AlignmentUtils.translatesAs(
+ "tttcccaaagggttt".toCharArray(), 0, "FPKG".toCharArray()));
+
+ // dna + stop codon + more
+ assertFalse(AlignmentUtils.translatesAs(
+ "tttcccaaagggttaga".toCharArray(), 0, "FPKG".toCharArray()));
+
+ // overlong protein
+ assertFalse(AlignmentUtils.translatesAs("tttcccaaaggg".toCharArray(),
+ 0, "FPKGQ".toCharArray()));
}
/**
assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
// now the other way round
- seq1.setDBRef(null);
+ seq1.setDBRefs(null);
seq2.addDBRef(new DBRefEntry("EMBL", "1", "A12345"));
assertTrue(AlignmentUtils.haveCrossRef(seq1, seq2));
assertTrue(AlignmentUtils.haveCrossRef(seq2, seq1));
}
/**
- * Test the method that extracts the exon-only part of a dna alignment.
+ * Test the method that extracts the cds-only part of a dna alignment.
*/
@Test(groups = { "Functional" })
- public void testMakeExonAlignment()
+ public void testMakeCdsAlignment()
{
SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
SequenceI dna2 = new Sequence("dna2", "GGGcccTTTaaaCCC");
dna2.createDatasetSequence();
pep1.createDatasetSequence();
pep2.createDatasetSequence();
+ dna1.addSequenceFeature(new SequenceFeature("CDS", "cds1", 4, 6, 0f,
+ null));
+ dna1.addSequenceFeature(new SequenceFeature("CDS", "cds2", 10, 12, 0f,
+ null));
+ dna2.addSequenceFeature(new SequenceFeature("CDS", "cds3", 1, 3, 0f,
+ null));
+ dna2.addSequenceFeature(new SequenceFeature("CDS", "cds4", 7, 9, 0f,
+ null));
+ dna2.addSequenceFeature(new SequenceFeature("CDS", "cds5", 13, 15, 0f,
+ null));
+ AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
+ dna.setDataset(null);
List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
MapList map = new MapList(new int[] { 4, 6, 10, 12 },
acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
mappings.add(acf);
- AlignmentI exons = AlignmentUtils.makeExonAlignment(new SequenceI[] {
- dna1, dna2 }, mappings);
- assertEquals(2, exons.getSequences().size());
- assertEquals("GGGTTT", exons.getSequenceAt(0).getSequenceAsString());
- assertEquals("GGGTTTCCC", exons.getSequenceAt(1).getSequenceAsString());
+ /*
+ * execute method under test:
+ */
+ AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
+ dna1, dna2 }, mappings, dna);
+
+ assertEquals(2, cds.getSequences().size());
+ assertEquals("GGGTTT", cds.getSequenceAt(0)
+ .getSequenceAsString());
+ assertEquals("GGGTTTCCC", cds.getSequenceAt(1)
+ .getSequenceAsString());
/*
- * Verify updated mappings
+ * verify shared, extended alignment dataset
*/
- assertEquals(2, mappings.size());
+ assertSame(dna.getDataset(), cds.getDataset());
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cds.getSequenceAt(0).getDatasetSequence()));
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cds.getSequenceAt(1).getDatasetSequence()));
/*
+ * Verify mappings from CDS to peptide and cDNA to CDS
+ * the mappings are on the shared alignment dataset
+ */
+ assertSame(dna.getCodonFrames(), cds.getCodonFrames());
+ List<AlignedCodonFrame> cdsMappings = cds.getCodonFrames();
+ assertEquals(2, cdsMappings.size());
+
+ /*
* Mapping from pep1 to GGGTTT in first new exon sequence
*/
List<AlignedCodonFrame> pep1Mapping = MappingUtils
- .findMappingsForSequence(pep1, mappings);
+ .findMappingsForSequence(pep1, cdsMappings);
assertEquals(1, pep1Mapping.size());
// map G to GGG
- SearchResults sr = MappingUtils.buildSearchResults(pep1, 1, mappings);
+ SearchResults sr = MappingUtils
+ .buildSearchResults(pep1, 1, cdsMappings);
assertEquals(1, sr.getResults().size());
Match m = sr.getResults().get(0);
- assertEquals(exons.getSequenceAt(0).getDatasetSequence(),
+ assertSame(cds.getSequenceAt(0).getDatasetSequence(),
m.getSequence());
assertEquals(1, m.getStart());
assertEquals(3, m.getEnd());
// map F to TTT
- sr = MappingUtils.buildSearchResults(pep1, 2, mappings);
+ sr = MappingUtils.buildSearchResults(pep1, 2, cdsMappings);
m = sr.getResults().get(0);
- assertEquals(exons.getSequenceAt(0).getDatasetSequence(),
+ assertSame(cds.getSequenceAt(0).getDatasetSequence(),
m.getSequence());
assertEquals(4, m.getStart());
assertEquals(6, m.getEnd());
* Mapping from pep2 to GGGTTTCCC in second new exon sequence
*/
List<AlignedCodonFrame> pep2Mapping = MappingUtils
- .findMappingsForSequence(pep2, mappings);
+ .findMappingsForSequence(pep2, cdsMappings);
assertEquals(1, pep2Mapping.size());
// map G to GGG
- sr = MappingUtils.buildSearchResults(pep2, 1, mappings);
+ sr = MappingUtils.buildSearchResults(pep2, 1, cdsMappings);
assertEquals(1, sr.getResults().size());
m = sr.getResults().get(0);
- assertEquals(exons.getSequenceAt(1).getDatasetSequence(),
+ assertSame(cds.getSequenceAt(1).getDatasetSequence(),
m.getSequence());
assertEquals(1, m.getStart());
assertEquals(3, m.getEnd());
// map F to TTT
- sr = MappingUtils.buildSearchResults(pep2, 2, mappings);
+ sr = MappingUtils.buildSearchResults(pep2, 2, cdsMappings);
m = sr.getResults().get(0);
- assertEquals(exons.getSequenceAt(1).getDatasetSequence(),
+ assertSame(cds.getSequenceAt(1).getDatasetSequence(),
m.getSequence());
assertEquals(4, m.getStart());
assertEquals(6, m.getEnd());
// map P to CCC
- sr = MappingUtils.buildSearchResults(pep2, 3, mappings);
+ sr = MappingUtils.buildSearchResults(pep2, 3, cdsMappings);
m = sr.getResults().get(0);
- assertEquals(exons.getSequenceAt(1).getDatasetSequence(),
+ assertSame(cds.getSequenceAt(1).getDatasetSequence(),
m.getSequence());
assertEquals(7, m.getStart());
assertEquals(9, m.getEnd());
}
/**
- * Test the method that makes an exon-only sequence from a DNA sequence and
- * its product mapping. Test includes the expected case that the DNA sequence
- * already has a protein product (Uniprot translation) which in turn has an
- * x-ref to the EMBLCDS record.
- */
- @Test(groups = { "Functional" })
- public void testMakeExonSequences()
- {
- SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
- SequenceI pep1 = new Sequence("pep1", "GF");
- dna1.createDatasetSequence();
- pep1.createDatasetSequence();
- pep1.getDatasetSequence().addDBRef(
- new DBRefEntry("EMBLCDS", "2", "A12345"));
-
- /*
- * Make the mapping from dna to protein. The protein sequence has a DBRef to
- * EMBLCDS|A12345.
- */
- Set<AlignedCodonFrame> mappings = new HashSet<AlignedCodonFrame>();
- MapList map = new MapList(new int[] { 4, 6, 10, 12 },
- new int[] { 1, 2 }, 3, 1);
- AlignedCodonFrame acf = new AlignedCodonFrame();
- acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
- mappings.add(acf);
-
- AlignedCodonFrame newMapping = new AlignedCodonFrame();
- List<SequenceI> exons = AlignmentUtils.makeExonSequences(dna1, acf,
- newMapping);
- assertEquals(1, exons.size());
- SequenceI exon = exons.get(0);
-
- assertEquals("GGGTTT", exon.getSequenceAsString());
- assertEquals("dna1|A12345", exon.getName());
- assertEquals(1, exon.getDBRef().length);
- DBRefEntry cdsRef = exon.getDBRef()[0];
- assertEquals("EMBLCDS", cdsRef.getSource());
- assertEquals("2", cdsRef.getVersion());
- assertEquals("A12345", cdsRef.getAccessionId());
- }
-
- /**
- * Test the method that makes an exon-only alignment from a DNA sequence and
- * its product mappings, for the case where there are multiple exon mappings
- * to different protein products.
+ * Test the method that makes a cds-only alignment from a DNA sequence and its
+ * product mappings, for the case where there are multiple exon mappings to
+ * different protein products.
*/
@Test(groups = { "Functional" })
- public void testMakeExonAlignment_multipleProteins()
+ public void testMakeCdsAlignment_multipleProteins()
{
SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
SequenceI pep1 = new Sequence("pep1", "GF"); // GGGTTT
pep1.createDatasetSequence();
pep2.createDatasetSequence();
pep3.createDatasetSequence();
+ dna1.addSequenceFeature(new SequenceFeature("CDS", "cds1", 4, 6, 0f,
+ null));
+ dna1.addSequenceFeature(new SequenceFeature("CDS", "cds2", 10, 12, 0f,
+ null));
+ dna1.addSequenceFeature(new SequenceFeature("CDS", "cds3", 1, 3, 0f,
+ null));
+ dna1.addSequenceFeature(new SequenceFeature("CDS", "cds4", 7, 9, 0f,
+ null));
+ dna1.addSequenceFeature(new SequenceFeature("CDS", "cds5", 1, 3, 0f,
+ null));
+ dna1.addSequenceFeature(new SequenceFeature("CDS", "cds6", 10, 12, 0f,
+ null));
pep1.getDatasetSequence().addDBRef(
new DBRefEntry("EMBLCDS", "2", "A12345"));
pep2.getDatasetSequence().addDBRef(
new DBRefEntry("EMBLCDS", "4", "A12347"));
/*
- * Make the mappings from dna to protein. Using LinkedHashset is a
- * convenience so results are in the input order. There is no assertion that
- * the generated exon sequences are in any particular order.
+ * Make the mappings from dna to protein
*/
List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
// map ...GGG...TTT to GF
mappings.add(acf);
/*
- * Create the Exon alignment; also replaces the dna-to-protein mappings with
+ * Create the CDS alignment; also augments the dna-to-protein mappings with
* exon-to-protein and exon-to-dna mappings
*/
- AlignmentI exal = AlignmentUtils.makeExonAlignment(
- new SequenceI[] { dna1 }, mappings);
+ AlignmentI dna = new Alignment(new SequenceI[] { dna1 });
+ dna.setDataset(null);
/*
- * Verify we have 3 exon sequences, mapped to pep1/2/3 respectively
+ * execute method under test
*/
- List<SequenceI> exons = exal.getSequences();
- assertEquals(3, exons.size());
+ AlignmentI cdsal = AlignmentUtils.makeCdsAlignment(
+ new SequenceI[] { dna1 }, mappings, dna);
- SequenceI exon = exons.get(0);
- assertEquals("GGGTTT", exon.getSequenceAsString());
- assertEquals("dna1|A12345", exon.getName());
- assertEquals(1, exon.getDBRef().length);
- DBRefEntry cdsRef = exon.getDBRef()[0];
- assertEquals("EMBLCDS", cdsRef.getSource());
- assertEquals("2", cdsRef.getVersion());
- assertEquals("A12345", cdsRef.getAccessionId());
+ /*
+ * Verify we have 3 cds sequences, mapped to pep1/2/3 respectively
+ */
+ List<SequenceI> cds = cdsal.getSequences();
+ assertEquals(3, cds.size());
- exon = exons.get(1);
- assertEquals("aaaccc", exon.getSequenceAsString());
- assertEquals("dna1|A12346", exon.getName());
- assertEquals(1, exon.getDBRef().length);
- cdsRef = exon.getDBRef()[0];
- assertEquals("EMBLCDS", cdsRef.getSource());
- assertEquals("3", cdsRef.getVersion());
- assertEquals("A12346", cdsRef.getAccessionId());
+ /*
+ * verify shared, extended alignment dataset
+ */
+ assertSame(cdsal.getDataset(), dna.getDataset());
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cds.get(0).getDatasetSequence()));
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cds.get(1).getDatasetSequence()));
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cds.get(2).getDatasetSequence()));
- exon = exons.get(2);
- assertEquals("aaaTTT", exon.getSequenceAsString());
- assertEquals("dna1|A12347", exon.getName());
- assertEquals(1, exon.getDBRef().length);
- cdsRef = exon.getDBRef()[0];
- assertEquals("EMBLCDS", cdsRef.getSource());
- assertEquals("4", cdsRef.getVersion());
- assertEquals("A12347", cdsRef.getAccessionId());
+ /*
+ * verify aligned cds sequences and their xrefs
+ */
+ SequenceI cdsSeq = cds.get(0);
+ assertEquals("GGGTTT", cdsSeq.getSequenceAsString());
+ // assertEquals("dna1|A12345", cdsSeq.getName());
+ assertEquals("dna1|pep1", cdsSeq.getName());
+ // assertEquals(1, cdsSeq.getDBRefs().length);
+ // DBRefEntry cdsRef = cdsSeq.getDBRefs()[0];
+ // assertEquals("EMBLCDS", cdsRef.getSource());
+ // assertEquals("2", cdsRef.getVersion());
+ // assertEquals("A12345", cdsRef.getAccessionId());
+
+ cdsSeq = cds.get(1);
+ assertEquals("aaaccc", cdsSeq.getSequenceAsString());
+ // assertEquals("dna1|A12346", cdsSeq.getName());
+ assertEquals("dna1|pep2", cdsSeq.getName());
+ // assertEquals(1, cdsSeq.getDBRefs().length);
+ // cdsRef = cdsSeq.getDBRefs()[0];
+ // assertEquals("EMBLCDS", cdsRef.getSource());
+ // assertEquals("3", cdsRef.getVersion());
+ // assertEquals("A12346", cdsRef.getAccessionId());
+
+ cdsSeq = cds.get(2);
+ assertEquals("aaaTTT", cdsSeq.getSequenceAsString());
+ // assertEquals("dna1|A12347", cdsSeq.getName());
+ assertEquals("dna1|pep3", cdsSeq.getName());
+ // assertEquals(1, cdsSeq.getDBRefs().length);
+ // cdsRef = cdsSeq.getDBRefs()[0];
+ // assertEquals("EMBLCDS", cdsRef.getSource());
+ // assertEquals("4", cdsRef.getVersion());
+ // assertEquals("A12347", cdsRef.getAccessionId());
/*
- * Verify there are mappings from each exon sequence to its protein product
+ * Verify there are mappings from each cds sequence to its protein product
* and also to its dna source
*/
- Iterator<AlignedCodonFrame> newMappingsIterator = mappings.iterator();
+ Iterator<AlignedCodonFrame> newMappingsIterator = cdsal
+ .getCodonFrames().iterator();
// mappings for dna1 - exon1 - pep1
- AlignedCodonFrame exonMapping = newMappingsIterator.next();
- List<Mapping> dnaMappings = exonMapping.getMappingsForSequence(dna1);
- assertEquals(1, dnaMappings.size());
- assertSame(exons.get(0).getDatasetSequence(), dnaMappings.get(0)
+ AlignedCodonFrame cdsMapping = newMappingsIterator.next();
+ List<Mapping> dnaMappings = cdsMapping.getMappingsFromSequence(dna1);
+ assertEquals(3, dnaMappings.size());
+ assertSame(cds.get(0).getDatasetSequence(), dnaMappings.get(0)
.getTo());
assertEquals("G(1) in CDS should map to G(4) in DNA", 4, dnaMappings
.get(0).getMap().getToPosition(1));
- List<Mapping> peptideMappings = exonMapping
- .getMappingsForSequence(pep1);
+ List<Mapping> peptideMappings = cdsMapping.getMappingsFromSequence(cds
+ .get(0).getDatasetSequence());
assertEquals(1, peptideMappings.size());
assertSame(pep1.getDatasetSequence(), peptideMappings.get(0).getTo());
- // mappings for dna1 - exon2 - pep2
- exonMapping = newMappingsIterator.next();
- dnaMappings = exonMapping.getMappingsForSequence(dna1);
- assertEquals(1, dnaMappings.size());
- assertSame(exons.get(1).getDatasetSequence(), dnaMappings.get(0)
+ // mappings for dna1 - cds2 - pep2
+ assertSame(cds.get(1).getDatasetSequence(), dnaMappings.get(1)
.getTo());
assertEquals("c(4) in CDS should map to c(7) in DNA", 7, dnaMappings
- .get(0).getMap().getToPosition(4));
- peptideMappings = exonMapping.getMappingsForSequence(pep2);
+ .get(1).getMap().getToPosition(4));
+ peptideMappings = cdsMapping.getMappingsFromSequence(cds.get(1)
+ .getDatasetSequence());
assertEquals(1, peptideMappings.size());
assertSame(pep2.getDatasetSequence(), peptideMappings.get(0).getTo());
- // mappings for dna1 - exon3 - pep3
- exonMapping = newMappingsIterator.next();
- dnaMappings = exonMapping.getMappingsForSequence(dna1);
- assertEquals(1, dnaMappings.size());
- assertSame(exons.get(2).getDatasetSequence(), dnaMappings.get(0)
+ // mappings for dna1 - cds3 - pep3
+ assertSame(cds.get(2).getDatasetSequence(), dnaMappings.get(2)
.getTo());
assertEquals("T(4) in CDS should map to T(10) in DNA", 10, dnaMappings
- .get(0).getMap().getToPosition(4));
- peptideMappings = exonMapping.getMappingsForSequence(pep3);
+ .get(2).getMap().getToPosition(4));
+ peptideMappings = cdsMapping.getMappingsFromSequence(cds.get(2)
+ .getDatasetSequence());
assertEquals(1, peptideMappings.size());
assertSame(pep3.getDatasetSequence(), peptideMappings.get(0).getTo());
}
* @throws IOException
*/
@Test(groups = { "Functional" })
- public void testMapProteinSequenceToCdna_forSubsequence()
+ public void testMapCdnaToProtein_forSubsequence()
throws IOException
{
SequenceI prot = new Sequence("UNIPROT|V12345", "E-I--Q", 10, 12);
SequenceI dna = new Sequence("EMBL|A33333", "GAA--AT-C-CAG", 40, 48);
dna.createDatasetSequence();
- MapList map = AlignmentUtils.mapProteinSequenceToCdna(prot, dna);
+ MapList map = AlignmentUtils.mapCdnaToProtein(prot, dna);
assertEquals(10, map.getToLowest());
assertEquals(12, map.getToHighest());
assertEquals(40, map.getFromLowest());
checkAlignSequenceAs("AAACCCTTT", "K-PFG", true, true, map,
"AAA---CCCTTT---");
}
+
+ /**
+ * Tests for transferring features between mapped sequences
+ */
+ @Test(groups = { "Functional" })
+ public void testTransferFeatures()
+ {
+ SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
+ SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
+
+ // no overlap
+ dna.addSequenceFeature(new SequenceFeature("type1", "desc1", 1, 2, 1f,
+ null));
+ // partial overlap - to [1, 1]
+ dna.addSequenceFeature(new SequenceFeature("type2", "desc2", 3, 4, 2f,
+ null));
+ // exact overlap - to [1, 3]
+ dna.addSequenceFeature(new SequenceFeature("type3", "desc3", 4, 6, 3f,
+ null));
+ // spanning overlap - to [2, 5]
+ dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
+ null));
+ // exactly overlaps whole mapped range [1, 6]
+ dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
+ null));
+ // no overlap (internal)
+ dna.addSequenceFeature(new SequenceFeature("type6", "desc6", 7, 9, 6f,
+ null));
+ // no overlap (3' end)
+ dna.addSequenceFeature(new SequenceFeature("type7", "desc7", 13, 15,
+ 7f, null));
+ // overlap (3' end) - to [6, 6]
+ dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
+ 8f, null));
+ // extended overlap - to [6, +]
+ dna.addSequenceFeature(new SequenceFeature("type9", "desc9", 12, 13,
+ 9f, null));
+
+ MapList map = new MapList(new int[] { 4, 6, 10, 12 },
+ new int[] { 1, 6 }, 1, 1);
+
+ /*
+ * transferFeatures() will build 'partial overlap' for regions
+ * that partially overlap 5' or 3' (start or end) of target sequence
+ */
+ AlignmentUtils.transferFeatures(dna, cds, map, null);
+ SequenceFeature[] sfs = cds.getSequenceFeatures();
+ assertEquals(6, sfs.length);
+
+ SequenceFeature sf = sfs[0];
+ assertEquals("type2", sf.getType());
+ assertEquals("desc2", sf.getDescription());
+ assertEquals(2f, sf.getScore());
+ assertEquals(1, sf.getBegin());
+ assertEquals(1, sf.getEnd());
+
+ sf = sfs[1];
+ assertEquals("type3", sf.getType());
+ assertEquals("desc3", sf.getDescription());
+ assertEquals(3f, sf.getScore());
+ assertEquals(1, sf.getBegin());
+ assertEquals(3, sf.getEnd());
+
+ sf = sfs[2];
+ assertEquals("type4", sf.getType());
+ assertEquals(2, sf.getBegin());
+ assertEquals(5, sf.getEnd());
+
+ sf = sfs[3];
+ assertEquals("type5", sf.getType());
+ assertEquals(1, sf.getBegin());
+ assertEquals(6, sf.getEnd());
+
+ sf = sfs[4];
+ assertEquals("type8", sf.getType());
+ assertEquals(6, sf.getBegin());
+ assertEquals(6, sf.getEnd());
+
+ sf = sfs[5];
+ assertEquals("type9", sf.getType());
+ assertEquals(6, sf.getBegin());
+ assertEquals(6, sf.getEnd());
+ }
+
+ /**
+ * Tests for transferring features between mapped sequences
+ */
+ @Test(groups = { "Functional" })
+ public void testTransferFeatures_withOmit()
+ {
+ SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
+ SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
+
+ MapList map = new MapList(new int[] { 4, 6, 10, 12 },
+ new int[] { 1, 6 }, 1, 1);
+
+ // [5, 11] maps to [2, 5]
+ dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
+ null));
+ // [4, 12] maps to [1, 6]
+ dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
+ null));
+ // [12, 12] maps to [6, 6]
+ dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
+ 8f, null));
+
+ // desc4 and desc8 are the 'omit these' varargs
+ AlignmentUtils.transferFeatures(dna, cds, map, null, "type4", "type8");
+ SequenceFeature[] sfs = cds.getSequenceFeatures();
+ assertEquals(1, sfs.length);
+
+ SequenceFeature sf = sfs[0];
+ assertEquals("type5", sf.getType());
+ assertEquals(1, sf.getBegin());
+ assertEquals(6, sf.getEnd());
+ }
+
+ /**
+ * Tests for transferring features between mapped sequences
+ */
+ @Test(groups = { "Functional" })
+ public void testTransferFeatures_withSelect()
+ {
+ SequenceI dna = new Sequence("dna/20-34", "acgTAGcaaGCCcgt");
+ SequenceI cds = new Sequence("cds/10-15", "TAGGCC");
+
+ MapList map = new MapList(new int[] { 4, 6, 10, 12 },
+ new int[] { 1, 6 }, 1, 1);
+
+ // [5, 11] maps to [2, 5]
+ dna.addSequenceFeature(new SequenceFeature("type4", "desc4", 5, 11, 4f,
+ null));
+ // [4, 12] maps to [1, 6]
+ dna.addSequenceFeature(new SequenceFeature("type5", "desc5", 4, 12, 5f,
+ null));
+ // [12, 12] maps to [6, 6]
+ dna.addSequenceFeature(new SequenceFeature("type8", "desc8", 12, 12,
+ 8f, null));
+
+ // "type5" is the 'select this type' argument
+ AlignmentUtils.transferFeatures(dna, cds, map, "type5");
+ SequenceFeature[] sfs = cds.getSequenceFeatures();
+ assertEquals(1, sfs.length);
+
+ SequenceFeature sf = sfs[0];
+ assertEquals("type5", sf.getType());
+ assertEquals(1, sf.getBegin());
+ assertEquals(6, sf.getEnd());
+ }
+
+ /**
+ * Test the method that extracts the cds-only part of a dna alignment, for the
+ * case where the cds should be aligned to match its nucleotide sequence.
+ */
+ @Test(groups = { "Functional" })
+ public void testMakeCdsAlignment_alternativeTranscripts()
+ {
+ SequenceI dna1 = new Sequence("dna1", "aaaGGGCC-----CTTTaaaGGG");
+ // alternative transcript of same dna skips CCC codon
+ SequenceI dna2 = new Sequence("dna2", "aaaGGGCC-----cttTaaaGGG");
+ // dna3 has no mapping (protein product) so should be ignored here
+ SequenceI dna3 = new Sequence("dna3", "aaaGGGCCCCCGGGcttTaaaGGG");
+ SequenceI pep1 = new Sequence("pep1", "GPFG");
+ SequenceI pep2 = new Sequence("pep2", "GPG");
+ dna1.createDatasetSequence();
+ dna2.createDatasetSequence();
+ dna3.createDatasetSequence();
+ pep1.createDatasetSequence();
+ pep2.createDatasetSequence();
+ dna1.addSequenceFeature(new SequenceFeature("CDS", "cds1", 4, 8, 0f,
+ null));
+ dna1.addSequenceFeature(new SequenceFeature("CDS", "cds2", 9, 12, 0f,
+ null));
+ dna1.addSequenceFeature(new SequenceFeature("CDS", "cds3", 16, 18, 0f,
+ null));
+ dna2.addSequenceFeature(new SequenceFeature("CDS", "cds", 4, 8, 0f,
+ null));
+ dna2.addSequenceFeature(new SequenceFeature("CDS", "cds", 12, 12, 0f,
+ null));
+ dna2.addSequenceFeature(new SequenceFeature("CDS", "cds", 16, 18, 0f,
+ null));
+
+ List<AlignedCodonFrame> mappings = new ArrayList<AlignedCodonFrame>();
+ MapList map = new MapList(new int[] { 4, 12, 16, 18 },
+ new int[] { 1, 4 }, 3, 1);
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ acf.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(), map);
+ mappings.add(acf);
+ map = new MapList(new int[] { 4, 8, 12, 12, 16, 18 },
+ new int[] { 1, 3 },
+ 3, 1);
+ acf = new AlignedCodonFrame();
+ acf.addMap(dna2.getDatasetSequence(), pep2.getDatasetSequence(), map);
+ mappings.add(acf);
+
+ AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
+ dna.setDataset(null);
+ AlignmentI cds = AlignmentUtils.makeCdsAlignment(new SequenceI[] {
+ dna1, dna2, dna3 }, mappings, dna);
+ List<SequenceI> cdsSeqs = cds.getSequences();
+ assertEquals(2, cdsSeqs.size());
+ assertEquals("GGGCCCTTTGGG", cdsSeqs.get(0).getSequenceAsString());
+ assertEquals("GGGCCTGGG", cdsSeqs.get(1).getSequenceAsString());
+
+ /*
+ * verify shared, extended alignment dataset
+ */
+ assertSame(dna.getDataset(), cds.getDataset());
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cdsSeqs.get(0).getDatasetSequence()));
+ assertTrue(dna.getDataset().getSequences()
+ .contains(cdsSeqs.get(1).getDatasetSequence()));
+
+ /*
+ * Verify updated mappings
+ */
+ List<AlignedCodonFrame> cdsMappings = cds.getCodonFrames();
+ assertEquals(2, cdsMappings.size());
+
+ /*
+ * Mapping from pep1 to GGGTTT in first new CDS sequence
+ */
+ List<AlignedCodonFrame> pep1Mapping = MappingUtils
+ .findMappingsForSequence(pep1, cdsMappings);
+ assertEquals(1, pep1Mapping.size());
+ /*
+ * maps GPFG to 1-3,4-6,7-9,10-12
+ */
+ SearchResults sr = MappingUtils
+ .buildSearchResults(pep1, 1, cdsMappings);
+ assertEquals(1, sr.getResults().size());
+ Match m = sr.getResults().get(0);
+ assertEquals(cds.getSequenceAt(0).getDatasetSequence(),
+ m.getSequence());
+ assertEquals(1, m.getStart());
+ assertEquals(3, m.getEnd());
+ sr = MappingUtils.buildSearchResults(pep1, 2, cdsMappings);
+ m = sr.getResults().get(0);
+ assertEquals(4, m.getStart());
+ assertEquals(6, m.getEnd());
+ sr = MappingUtils.buildSearchResults(pep1, 3, cdsMappings);
+ m = sr.getResults().get(0);
+ assertEquals(7, m.getStart());
+ assertEquals(9, m.getEnd());
+ sr = MappingUtils.buildSearchResults(pep1, 4, cdsMappings);
+ m = sr.getResults().get(0);
+ assertEquals(10, m.getStart());
+ assertEquals(12, m.getEnd());
+
+ /*
+ * GPG in pep2 map to 1-3,4-6,7-9 in second CDS sequence
+ */
+ List<AlignedCodonFrame> pep2Mapping = MappingUtils
+ .findMappingsForSequence(pep2, cdsMappings);
+ assertEquals(1, pep2Mapping.size());
+ sr = MappingUtils.buildSearchResults(pep2, 1, cdsMappings);
+ assertEquals(1, sr.getResults().size());
+ m = sr.getResults().get(0);
+ assertEquals(cds.getSequenceAt(1).getDatasetSequence(),
+ m.getSequence());
+ assertEquals(1, m.getStart());
+ assertEquals(3, m.getEnd());
+ sr = MappingUtils.buildSearchResults(pep2, 2, cdsMappings);
+ m = sr.getResults().get(0);
+ assertEquals(4, m.getStart());
+ assertEquals(6, m.getEnd());
+ sr = MappingUtils.buildSearchResults(pep2, 3, cdsMappings);
+ m = sr.getResults().get(0);
+ assertEquals(7, m.getStart());
+ assertEquals(9, m.getEnd());
+ }
+
+ /**
+ * Test the method that realigns protein to match mapped codon alignment.
+ */
+ @Test(groups = { "Functional" })
+ public void testAlignProteinAsDna_incompleteStartCodon()
+ {
+ // seq1: incomplete start codon (not mapped), then [3, 11]
+ SequenceI dna1 = new Sequence("Seq1", "ccAAA-TTT-GGG-");
+ // seq2 codons are [4, 5], [8, 11]
+ SequenceI dna2 = new Sequence("Seq2", "ccaAA-ttT-GGG-");
+ // seq3 incomplete start codon at 'tt'
+ SequenceI dna3 = new Sequence("Seq3", "ccaaa-ttt-GGG-");
+ AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2, dna3 });
+ dna.setDataset(null);
+
+ // prot1 has 'X' for incomplete start codon (not mapped)
+ SequenceI prot1 = new Sequence("Seq1", "XKFG"); // X for incomplete start
+ SequenceI prot2 = new Sequence("Seq2", "NG");
+ SequenceI prot3 = new Sequence("Seq3", "XG"); // X for incomplete start
+ AlignmentI protein = new Alignment(new SequenceI[] { prot1, prot2,
+ prot3 });
+ protein.setDataset(null);
+
+ // map dna1 [3, 11] to prot1 [2, 4] KFG
+ MapList map = new MapList(new int[] { 3, 11 }, new int[] { 2, 4 }, 3, 1);
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ acf.addMap(dna1.getDatasetSequence(), prot1.getDatasetSequence(), map);
+
+ // map dna2 [4, 5] [8, 11] to prot2 [1, 2] NG
+ map = new MapList(new int[] { 4, 5, 8, 11 }, new int[] { 1, 2 }, 3, 1);
+ acf.addMap(dna2.getDatasetSequence(), prot2.getDatasetSequence(), map);
+
+ // map dna3 [9, 11] to prot3 [2, 2] G
+ map = new MapList(new int[] { 9, 11 }, new int[] { 2, 2 }, 3, 1);
+ acf.addMap(dna3.getDatasetSequence(), prot3.getDatasetSequence(), map);
+
+ ArrayList<AlignedCodonFrame> acfs = new ArrayList<AlignedCodonFrame>();
+ acfs.add(acf);
+ protein.setCodonFrames(acfs);
+
+ /*
+ * verify X is included in the aligned proteins, and placed just
+ * before the first mapped residue
+ * CCT is between CCC and TTT
+ */
+ AlignmentUtils.alignProteinAsDna(protein, dna);
+ assertEquals("XK-FG", prot1.getSequenceAsString());
+ assertEquals("--N-G", prot2.getSequenceAsString());
+ assertEquals("---XG", prot3.getSequenceAsString());
+ }
+
+ /**
+ * Tests for the method that maps the subset of a dna sequence that has CDS
+ * (or subtype) feature - case where the start codon is incomplete.
+ */
+ @Test(groups = "Functional")
+ public void testFindCdsPositions_fivePrimeIncomplete()
+ {
+ SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
+ dnaSeq.createDatasetSequence();
+ SequenceI ds = dnaSeq.getDatasetSequence();
+
+ // CDS for dna 5-6 (incomplete codon), 7-9
+ SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
+ sf.setPhase("2"); // skip 2 bases to start of next codon
+ ds.addSequenceFeature(sf);
+ // CDS for dna 13-15
+ sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
+ ds.addSequenceFeature(sf);
+
+ List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
+
+ /*
+ * check the mapping starts with the first complete codon
+ */
+ assertEquals(6, MappingUtils.getLength(ranges));
+ assertEquals(2, ranges.size());
+ assertEquals(7, ranges.get(0)[0]);
+ assertEquals(9, ranges.get(0)[1]);
+ assertEquals(13, ranges.get(1)[0]);
+ assertEquals(15, ranges.get(1)[1]);
+ }
+
+ /**
+ * Tests for the method that maps the subset of a dna sequence that has CDS
+ * (or subtype) feature.
+ */
+ @Test(groups = "Functional")
+ public void testFindCdsPositions()
+ {
+ SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
+ dnaSeq.createDatasetSequence();
+ SequenceI ds = dnaSeq.getDatasetSequence();
+
+ // CDS for dna 10-12
+ SequenceFeature sf = new SequenceFeature("CDS_predicted", "", 10, 12,
+ 0f, null);
+ sf.setStrand("+");
+ ds.addSequenceFeature(sf);
+ // CDS for dna 4-6
+ sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
+ sf.setStrand("+");
+ ds.addSequenceFeature(sf);
+ // exon feature should be ignored here
+ sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
+ ds.addSequenceFeature(sf);
+
+ List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
+ /*
+ * verify ranges { [4-6], [12-10] }
+ * note CDS ranges are ordered ascending even if the CDS
+ * features are not
+ */
+ assertEquals(6, MappingUtils.getLength(ranges));
+ assertEquals(2, ranges.size());
+ assertEquals(4, ranges.get(0)[0]);
+ assertEquals(6, ranges.get(0)[1]);
+ assertEquals(10, ranges.get(1)[0]);
+ assertEquals(12, ranges.get(1)[1]);
+ }
+
+ /**
+ * Test the method that computes a map of codon variants for each protein
+ * position from "sequence_variant" features on dna
+ */
+ @Test(groups = "Functional")
+ public void testBuildDnaVariantsMap()
+ {
+ SequenceI dna = new Sequence("dna", "atgAAATTTGGGCCCtag");
+ MapList map = new MapList(new int[] { 1, 18 }, new int[] { 1, 5 }, 3, 1);
+
+ /*
+ * first with no variants on dna
+ */
+ LinkedHashMap<Integer, List<DnaVariant>[]> variantsMap = AlignmentUtils
+ .buildDnaVariantsMap(dna, map);
+ assertTrue(variantsMap.isEmpty());
+
+ /*
+ * single allele codon 1, on base 1
+ */
+ SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1,
+ 0f, null);
+ sf1.setValue("alleles", "T");
+ sf1.setValue("ID", "sequence_variant:rs758803211");
+ dna.addSequenceFeature(sf1);
+
+ /*
+ * two alleles codon 2, on bases 2 and 3 (distinct variants)
+ */
+ SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 5, 5,
+ 0f, null);
+ sf2.setValue("alleles", "T");
+ sf2.setValue("ID", "sequence_variant:rs758803212");
+ dna.addSequenceFeature(sf2);
+ SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 6, 6,
+ 0f, null);
+ sf3.setValue("alleles", "G");
+ sf3.setValue("ID", "sequence_variant:rs758803213");
+ dna.addSequenceFeature(sf3);
+
+ /*
+ * two alleles codon 3, both on base 2 (one variant)
+ */
+ SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 8, 8,
+ 0f, null);
+ sf4.setValue("alleles", "C, G");
+ sf4.setValue("ID", "sequence_variant:rs758803214");
+ dna.addSequenceFeature(sf4);
+
+ // no alleles on codon 4
+
+ /*
+ * alleles on codon 5 on all 3 bases (distinct variants)
+ */
+ SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 13,
+ 13, 0f, null);
+ sf5.setValue("alleles", "C, G"); // (C duplicates given base value)
+ sf5.setValue("ID", "sequence_variant:rs758803215");
+ dna.addSequenceFeature(sf5);
+ SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 14,
+ 14, 0f, null);
+ sf6.setValue("alleles", "g, a"); // should force to upper-case
+ sf6.setValue("ID", "sequence_variant:rs758803216");
+ dna.addSequenceFeature(sf6);
+ SequenceFeature sf7 = new SequenceFeature("sequence_variant", "", 15,
+ 15, 0f, null);
+ sf7.setValue("alleles", "A, T");
+ sf7.setValue("ID", "sequence_variant:rs758803217");
+ dna.addSequenceFeature(sf7);
+
+ /*
+ * build map - expect variants on positions 1, 2, 3, 5
+ */
+ variantsMap = AlignmentUtils.buildDnaVariantsMap(dna, map);
+ assertEquals(4, variantsMap.size());
+
+ /*
+ * protein residue 1: variant on codon (ATG) base 1, not on 2 or 3
+ */
+ List<DnaVariant>[] pep1Variants = variantsMap.get(1);
+ assertEquals(3, pep1Variants.length);
+ assertEquals(1, pep1Variants[0].size());
+ assertEquals("A", pep1Variants[0].get(0).base); // codon[1] base
+ assertSame(sf1, pep1Variants[0].get(0).variant); // codon[1] variant
+ assertEquals(1, pep1Variants[1].size());
+ assertEquals("T", pep1Variants[1].get(0).base); // codon[2] base
+ assertNull(pep1Variants[1].get(0).variant); // no variant here
+ assertEquals(1, pep1Variants[2].size());
+ assertEquals("G", pep1Variants[2].get(0).base); // codon[3] base
+ assertNull(pep1Variants[2].get(0).variant); // no variant here
+
+ /*
+ * protein residue 2: variants on codon (AAA) bases 2 and 3
+ */
+ List<DnaVariant>[] pep2Variants = variantsMap.get(2);
+ assertEquals(3, pep2Variants.length);
+ assertEquals(1, pep2Variants[0].size());
+ // codon[1] base recorded while processing variant on codon[2]
+ assertEquals("A", pep2Variants[0].get(0).base);
+ assertNull(pep2Variants[0].get(0).variant); // no variant here
+ // codon[2] base and variant:
+ assertEquals(1, pep2Variants[1].size());
+ assertEquals("A", pep2Variants[1].get(0).base);
+ assertSame(sf2, pep2Variants[1].get(0).variant);
+ // codon[3] base was recorded when processing codon[2] variant
+ // and then the variant for codon[3] added to it
+ assertEquals(1, pep2Variants[2].size());
+ assertEquals("A", pep2Variants[2].get(0).base);
+ assertSame(sf3, pep2Variants[2].get(0).variant);
+
+ /*
+ * protein residue 3: variants on codon (TTT) base 2 only
+ */
+ List<DnaVariant>[] pep3Variants = variantsMap.get(3);
+ assertEquals(3, pep3Variants.length);
+ assertEquals(1, pep3Variants[0].size());
+ assertEquals("T", pep3Variants[0].get(0).base); // codon[1] base
+ assertNull(pep3Variants[0].get(0).variant); // no variant here
+ assertEquals(1, pep3Variants[1].size());
+ assertEquals("T", pep3Variants[1].get(0).base); // codon[2] base
+ assertSame(sf4, pep3Variants[1].get(0).variant); // codon[2] variant
+ assertEquals(1, pep3Variants[2].size());
+ assertEquals("T", pep3Variants[2].get(0).base); // codon[3] base
+ assertNull(pep3Variants[2].get(0).variant); // no variant here
+
+ /*
+ * three variants on protein position 5
+ */
+ List<DnaVariant>[] pep5Variants = variantsMap.get(5);
+ assertEquals(3, pep5Variants.length);
+ assertEquals(1, pep5Variants[0].size());
+ assertEquals("C", pep5Variants[0].get(0).base); // codon[1] base
+ assertSame(sf5, pep5Variants[0].get(0).variant); // codon[1] variant
+ assertEquals(1, pep5Variants[1].size());
+ assertEquals("C", pep5Variants[1].get(0).base); // codon[2] base
+ assertSame(sf6, pep5Variants[1].get(0).variant); // codon[2] variant
+ assertEquals(1, pep5Variants[2].size());
+ assertEquals("C", pep5Variants[2].get(0).base); // codon[3] base
+ assertSame(sf7, pep5Variants[2].get(0).variant); // codon[3] variant
+ }
+
+ /**
+ * Tests for the method that computes all peptide variants given codon
+ * variants
+ */
+ @Test(groups = "Functional")
+ public void testComputePeptideVariants()
+ {
+ /*
+ * scenario: AAATTTCCC codes for KFP, with variants
+ * GAA -> E
+ * CAA -> Q
+ * AAG synonymous
+ * AAT -> N
+ * TTC synonymous
+ * CAC,CGC -> H,R (as one variant)
+ */
+ SequenceI peptide = new Sequence("pep/10-12", "KFP");
+
+ /*
+ * two distinct variants for codon 1 position 1
+ * second one has clinical significance
+ */
+ SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1,
+ 0f, null);
+ sf1.setValue("alleles", "A,G"); // GAA -> E
+ sf1.setValue("ID", "var1.125A>G");
+ SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 1, 1,
+ 0f, null);
+ sf2.setValue("alleles", "A,C"); // CAA -> Q
+ sf2.setValue("ID", "var2");
+ sf2.setValue("clinical_significance", "Dodgy");
+ SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 3, 3,
+ 0f, null);
+ sf3.setValue("alleles", "A,G"); // synonymous
+ sf3.setValue("ID", "var3");
+ sf3.setValue("clinical_significance", "None");
+ SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 3, 3,
+ 0f, null);
+ sf4.setValue("alleles", "A,T"); // AAT -> N
+ sf4.setValue("ID", "sequence_variant:var4"); // prefix gets stripped off
+ sf4.setValue("clinical_significance", "Benign");
+ SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 6, 6,
+ 0f, null);
+ sf5.setValue("alleles", "T,C"); // synonymous
+ sf5.setValue("ID", "var5");
+ sf5.setValue("clinical_significance", "Bad");
+ SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 8, 8,
+ 0f, null);
+ sf6.setValue("alleles", "C,A,G"); // CAC,CGC -> H,R
+ sf6.setValue("ID", "var6");
+ sf6.setValue("clinical_significance", "Good");
+
+ List<DnaVariant> codon1Variants = new ArrayList<DnaVariant>();
+ List<DnaVariant> codon2Variants = new ArrayList<DnaVariant>();
+ List<DnaVariant> codon3Variants = new ArrayList<DnaVariant>();
+ List<DnaVariant> codonVariants[] = new ArrayList[3];
+ codonVariants[0] = codon1Variants;
+ codonVariants[1] = codon2Variants;
+ codonVariants[2] = codon3Variants;
+
+ /*
+ * compute variants for protein position 1
+ */
+ codon1Variants.add(new DnaVariant("A", sf1));
+ codon1Variants.add(new DnaVariant("A", sf2));
+ codon2Variants.add(new DnaVariant("A"));
+ codon2Variants.add(new DnaVariant("A"));
+ codon3Variants.add(new DnaVariant("A", sf3));
+ codon3Variants.add(new DnaVariant("A", sf4));
+ AlignmentUtils.computePeptideVariants(peptide, 1, codonVariants);
+
+ /*
+ * compute variants for protein position 2
+ */
+ codon1Variants.clear();
+ codon2Variants.clear();
+ codon3Variants.clear();
+ codon1Variants.add(new DnaVariant("T"));
+ codon2Variants.add(new DnaVariant("T"));
+ codon3Variants.add(new DnaVariant("T", sf5));
+ AlignmentUtils.computePeptideVariants(peptide, 2, codonVariants);
+
+ /*
+ * compute variants for protein position 3
+ */
+ codon1Variants.clear();
+ codon2Variants.clear();
+ codon3Variants.clear();
+ codon1Variants.add(new DnaVariant("C"));
+ codon2Variants.add(new DnaVariant("C", sf6));
+ codon3Variants.add(new DnaVariant("C"));
+ AlignmentUtils.computePeptideVariants(peptide, 3, codonVariants);
+
+ /*
+ * verify added sequence features for
+ * var1 K -> E
+ * var2 K -> Q
+ * var4 K -> N
+ * var6 P -> H
+ * var6 P -> R
+ */
+ SequenceFeature[] sfs = peptide.getSequenceFeatures();
+ assertEquals(5, sfs.length);
+ SequenceFeature sf = sfs[0];
+ assertEquals(1, sf.getBegin());
+ assertEquals(1, sf.getEnd());
+ assertEquals("p.Lys1Glu", sf.getDescription());
+ assertEquals("var1.125A>G", sf.getValue("ID"));
+ assertNull(sf.getValue("clinical_significance"));
+ assertEquals("ID=var1.125A>G", sf.getAttributes());
+ assertEquals(1, sf.links.size());
+ // link to variation is urlencoded
+ assertEquals(
+ "p.Lys1Glu var1.125A>G|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var1.125A%3EG",
+ sf.links.get(0));
+ assertEquals("Jalview", sf.getFeatureGroup());
+ sf = sfs[1];
+ assertEquals(1, sf.getBegin());
+ assertEquals(1, sf.getEnd());
+ assertEquals("p.Lys1Gln", sf.getDescription());
+ assertEquals("var2", sf.getValue("ID"));
+ assertEquals("Dodgy", sf.getValue("clinical_significance"));
+ assertEquals("ID=var2;clinical_significance=Dodgy", sf.getAttributes());
+ assertEquals(1, sf.links.size());
+ assertEquals(
+ "p.Lys1Gln var2|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var2",
+ sf.links.get(0));
+ assertEquals("Jalview", sf.getFeatureGroup());
+ sf = sfs[2];
+ assertEquals(1, sf.getBegin());
+ assertEquals(1, sf.getEnd());
+ assertEquals("p.Lys1Asn", sf.getDescription());
+ assertEquals("var4", sf.getValue("ID"));
+ assertEquals("Benign", sf.getValue("clinical_significance"));
+ assertEquals("ID=var4;clinical_significance=Benign", sf.getAttributes());
+ assertEquals(1, sf.links.size());
+ assertEquals(
+ "p.Lys1Asn var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
+ sf.links.get(0));
+ assertEquals("Jalview", sf.getFeatureGroup());
+ sf = sfs[3];
+ assertEquals(3, sf.getBegin());
+ assertEquals(3, sf.getEnd());
+ assertEquals("p.Pro3His", sf.getDescription());
+ assertEquals("var6", sf.getValue("ID"));
+ assertEquals("Good", sf.getValue("clinical_significance"));
+ assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes());
+ assertEquals(1, sf.links.size());
+ assertEquals(
+ "p.Pro3His var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
+ sf.links.get(0));
+ // var5 generates two distinct protein variant features
+ assertEquals("Jalview", sf.getFeatureGroup());
+ sf = sfs[4];
+ assertEquals(3, sf.getBegin());
+ assertEquals(3, sf.getEnd());
+ assertEquals("p.Pro3Arg", sf.getDescription());
+ assertEquals("var6", sf.getValue("ID"));
+ assertEquals("Good", sf.getValue("clinical_significance"));
+ assertEquals("ID=var6;clinical_significance=Good", sf.getAttributes());
+ assertEquals(1, sf.links.size());
+ assertEquals(
+ "p.Pro3Arg var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
+ sf.links.get(0));
+ assertEquals("Jalview", sf.getFeatureGroup());
+ }
+
+ /**
+ * Tests for the method that maps the subset of a dna sequence that has CDS
+ * (or subtype) feature, with CDS strand = '-' (reverse)
+ */
+ // test turned off as currently findCdsPositions is not strand-dependent
+ // left in case it comes around again...
+ @Test(groups = "Functional", enabled = false)
+ public void testFindCdsPositions_reverseStrand()
+ {
+ SequenceI dnaSeq = new Sequence("dna", "aaaGGGcccAAATTTttt");
+ dnaSeq.createDatasetSequence();
+ SequenceI ds = dnaSeq.getDatasetSequence();
+
+ // CDS for dna 4-6
+ SequenceFeature sf = new SequenceFeature("CDS", "", 4, 6, 0f, null);
+ sf.setStrand("-");
+ ds.addSequenceFeature(sf);
+ // exon feature should be ignored here
+ sf = new SequenceFeature("exon", "", 7, 9, 0f, null);
+ ds.addSequenceFeature(sf);
+ // CDS for dna 10-12
+ sf = new SequenceFeature("CDS_predicted", "", 10, 12, 0f, null);
+ sf.setStrand("-");
+ ds.addSequenceFeature(sf);
+
+ List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
+ /*
+ * verify ranges { [12-10], [6-4] }
+ */
+ assertEquals(6, MappingUtils.getLength(ranges));
+ assertEquals(2, ranges.size());
+ assertEquals(12, ranges.get(0)[0]);
+ assertEquals(10, ranges.get(0)[1]);
+ assertEquals(6, ranges.get(1)[0]);
+ assertEquals(4, ranges.get(1)[1]);
+ }
+
+ /**
+ * Tests for the method that maps the subset of a dna sequence that has CDS
+ * (or subtype) feature - reverse strand case where the start codon is
+ * incomplete.
+ */
+ @Test(groups = "Functional", enabled = false)
+ // test turned off as currently findCdsPositions is not strand-dependent
+ // left in case it comes around again...
+ public void testFindCdsPositions_reverseStrandThreePrimeIncomplete()
+ {
+ SequenceI dnaSeq = new Sequence("dna", "aaagGGCCCaaaTTTttt");
+ dnaSeq.createDatasetSequence();
+ SequenceI ds = dnaSeq.getDatasetSequence();
+
+ // CDS for dna 5-9
+ SequenceFeature sf = new SequenceFeature("CDS", "", 5, 9, 0f, null);
+ sf.setStrand("-");
+ ds.addSequenceFeature(sf);
+ // CDS for dna 13-15
+ sf = new SequenceFeature("CDS_predicted", "", 13, 15, 0f, null);
+ sf.setStrand("-");
+ sf.setPhase("2"); // skip 2 bases to start of next codon
+ ds.addSequenceFeature(sf);
+
+ List<int[]> ranges = AlignmentUtils.findCdsPositions(dnaSeq);
+
+ /*
+ * check the mapping starts with the first complete codon
+ * expect ranges [13, 13], [9, 5]
+ */
+ assertEquals(6, MappingUtils.getLength(ranges));
+ assertEquals(2, ranges.size());
+ assertEquals(13, ranges.get(0)[0]);
+ assertEquals(13, ranges.get(0)[1]);
+ assertEquals(9, ranges.get(1)[0]);
+ assertEquals(5, ranges.get(1)[1]);
+ }
+
+ @Test(groups = "Functional")
+ public void testAlignAs_alternateTranscriptsUngapped()
+ {
+ SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
+ SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
+ AlignmentI dna = new Alignment(new SequenceI[] { dna1, dna2 });
+ ((Alignment) dna).createDatasetAlignment();
+ SequenceI cds1 = new Sequence("cds1", "GGGTTT");
+ SequenceI cds2 = new Sequence("cds2", "CCCAAA");
+ AlignmentI cds = new Alignment(new SequenceI[] { cds1, cds2 });
+ ((Alignment) cds).createDatasetAlignment();
+
+ AlignedCodonFrame acf = new AlignedCodonFrame();
+ MapList map = new MapList(new int[] { 4, 9 }, new int[] { 1, 6 }, 1, 1);
+ acf.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(), map);
+ map = new MapList(new int[] { 1, 3, 10, 12 }, new int[] { 1, 6 }, 1, 1);
+ acf.addMap(dna2.getDatasetSequence(), cds2.getDatasetSequence(), map);
+
+ /*
+ * verify CDS alignment is as:
+ * cccGGGTTTaaa (cdna)
+ * CCCgggtttAAA (cdna)
+ *
+ * ---GGGTTT--- (cds)
+ * CCC------AAA (cds)
+ */
+ dna.addCodonFrame(acf);
+ AlignmentUtils.alignAs(cds, dna);
+ assertEquals("---GGGTTT", cds.getSequenceAt(0).getSequenceAsString());
+ assertEquals("CCC------AAA", cds.getSequenceAt(1).getSequenceAsString());
+ }
+
+ @Test(groups = { "Functional" })
+ public void testAddMappedPositions()
+ {
+ SequenceI from = new Sequence("dna", "ggAA-ATcc-TT-g");
+ SequenceI seq1 = new Sequence("cds", "AAATTT");
+ from.createDatasetSequence();
+ seq1.createDatasetSequence();
+ Mapping mapping = new Mapping(seq1, new MapList(
+ new int[] { 3, 6, 9, 10 },
+ new int[] { 1, 6 }, 1, 1));
+ Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
+ AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
+
+ /*
+ * verify map has seq1 residues in columns 3,4,6,7,11,12
+ */
+ assertEquals(6, map.size());
+ assertEquals('A', map.get(3).get(seq1).charValue());
+ assertEquals('A', map.get(4).get(seq1).charValue());
+ assertEquals('A', map.get(6).get(seq1).charValue());
+ assertEquals('T', map.get(7).get(seq1).charValue());
+ assertEquals('T', map.get(11).get(seq1).charValue());
+ assertEquals('T', map.get(12).get(seq1).charValue());
+
+ /*
+ *
+ */
+ }
+
+ /**
+ * Test case where the mapping 'from' range includes a stop codon which is
+ * absent in the 'to' range
+ */
+ @Test(groups = { "Functional" })
+ public void testAddMappedPositions_withStopCodon()
+ {
+ SequenceI from = new Sequence("dna", "ggAA-ATcc-TT-g");
+ SequenceI seq1 = new Sequence("cds", "AAATTT");
+ from.createDatasetSequence();
+ seq1.createDatasetSequence();
+ Mapping mapping = new Mapping(seq1, new MapList(
+ new int[] { 3, 6, 9, 10 },
+ new int[] { 1, 6 }, 1, 1));
+ Map<Integer, Map<SequenceI, Character>> map = new TreeMap<Integer, Map<SequenceI, Character>>();
+ AlignmentUtils.addMappedPositions(seq1, from, mapping, map);
+
+ /*
+ * verify map has seq1 residues in columns 3,4,6,7,11,12
+ */
+ assertEquals(6, map.size());
+ assertEquals('A', map.get(3).get(seq1).charValue());
+ assertEquals('A', map.get(4).get(seq1).charValue());
+ assertEquals('A', map.get(6).get(seq1).charValue());
+ assertEquals('T', map.get(7).get(seq1).charValue());
+ assertEquals('T', map.get(11).get(seq1).charValue());
+ assertEquals('T', map.get(12).get(seq1).charValue());
+ }
}
git://source.jalview.org / jalview.git / blobdiff