*/
package jalview.analysis;
+import static org.junit.Assert.assertNotEquals;
import static org.testng.AssertJUnit.assertEquals;
import static org.testng.AssertJUnit.assertFalse;
import static org.testng.AssertJUnit.assertNotNull;
import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.datamodel.AlignedCodonFrame.SequenceToSequenceMapping;
import jalview.datamodel.features.SequenceFeatures;
import jalview.gui.JvOptionPane;
import jalview.io.AppletFormatAdapter;
import jalview.io.FileFormat;
import jalview.io.FileFormatI;
import jalview.io.FormatAdapter;
+import jalview.io.gff.SequenceOntologyI;
import jalview.util.MapList;
import jalview.util.MappingUtils;
import java.io.IOException;
import java.util.ArrayList;
import java.util.Arrays;
+import java.util.Iterator;
import java.util.LinkedHashMap;
import java.util.List;
import java.util.Map;
ArrayList<AlignedCodonFrame> acfs = new ArrayList<>();
acfs.add(acf);
protein.setCodonFrames(acfs);
-
+ Iterator<SequenceI> protseq = protein.getSequences().iterator();
+ for (SequenceI dnaseq:dna.getSequences()) {
+ assertCanResolveProteinCDS(dnaseq,protseq.next(),protein);
+ }
/*
* verify X is included in the aligned proteins, and placed just
* before the first mapped residue
}
/**
+ * assert that we can resolve the protein product in the given alignment given a DNA sequence with CDS mapping
+ * @param dnaseq
+ * @param protein
+ */
+ private void assertCanResolveProteinCDS(SequenceI dnaseq, SequenceI expProtein, AlignmentI protein)
+ {
+ // try a few different methods to check all work
+ SequenceI aprot=null;
+ for (AlignedCodonFrame cf:protein.getCodonFrame(dnaseq))
+ {
+ aprot=cf.getAaForDnaSeq(dnaseq);
+ if (aprot!=null)
+ {
+ assertTrue("getAaForDnaSeq didn't return expected protein sequence",aprot!=expProtein);
+ break;
+ }
+ }
+ assertNotNull("Didn't locate any proteins via AlignmentI.getCodonFrame .. AlignCodonFrame.getAaForDnaSeq", aprot);
+ // try mapping utils -
+ List<AlignedCodonFrame> mu_mappings=MappingUtils.findMappingsForSequence(dnaseq, protein.getCodonFrames());
+ assertNotNull("No mappings found for dnaseq in protein alignment via MappingUtils.findMappingsForSequence",mu_mappings);
+ assertNotEquals("No mappings found for dnaseq in protein alignment via MappingUtils.findMappingsForSequence",0,mu_mappings.size());
+ SequenceI mu_alignedprot=null;
+ List<SequenceToSequenceMapping> foundMap=null;
+ for (AlignedCodonFrame cf:mu_mappings)
+ {
+ foundMap=new ArrayList<>();
+ mu_alignedprot = cf.findAlignedSequence(dnaseq, protein,foundMap);
+ if (mu_alignedprot!=null) {
+ break;
+ }
+ }
+ assertNotNull("Didn't locate proteins via MappingUtils.findMappingsForSequence",mu_alignedprot);
+ assertTrue("findAlignedSequence didn't return expected protein sequence",mu_alignedprot==expProtein);
+ }
+
+ /**
* 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 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
- * variants:
- * GAA -> E source: Ensembl
- * CAA -> Q source: dbSNP
- * TAA -> STOP source: dnSNP
- * AAG synonymous source: COSMIC
- * AAT -> N source: Ensembl
- * ...TTC synonymous source: dbSNP
- * ......CAC,CGC -> H,R source: COSMIC
- * (one variant with two alleles)
- */
- SequenceI peptide = new Sequence("pep/10-12", "KFP");
-
- /*
- * two distinct variants for codon 1 position 1
- * second one has clinical significance
- */
- String ensembl = "Ensembl";
- String dbSnp = "dbSNP";
- String cosmic = "COSMIC";
-
- SequenceFeature sf1 = new SequenceFeature("sequence_variant", "", 1, 1,
- 0f, ensembl);
- sf1.setValue("alleles", "A,G"); // AAA -> GAA -> K/E
- sf1.setValue("ID", "var1.125A>G");
-
- SequenceFeature sf2 = new SequenceFeature("sequence_variant", "", 1, 1,
- 0f, dbSnp);
- sf2.setValue("alleles", "A,C"); // AAA -> CAA -> K/Q
- sf2.setValue("ID", "var2");
- sf2.setValue("clinical_significance", "Dodgy");
-
- SequenceFeature sf3 = new SequenceFeature("sequence_variant", "", 1, 1,
- 0f, dbSnp);
- sf3.setValue("alleles", "A,T"); // AAA -> TAA -> stop codon
- sf3.setValue("ID", "var3");
- sf3.setValue("clinical_significance", "Bad");
-
- SequenceFeature sf4 = new SequenceFeature("sequence_variant", "", 3, 3,
- 0f, cosmic);
- sf4.setValue("alleles", "A,G"); // AAA -> AAG synonymous
- sf4.setValue("ID", "var4");
- sf4.setValue("clinical_significance", "None");
-
- SequenceFeature sf5 = new SequenceFeature("sequence_variant", "", 3, 3,
- 0f, ensembl);
- sf5.setValue("alleles", "A,T"); // AAA -> AAT -> K/N
- sf5.setValue("ID", "sequence_variant:var5"); // prefix gets stripped off
- sf5.setValue("clinical_significance", "Benign");
-
- SequenceFeature sf6 = new SequenceFeature("sequence_variant", "", 6, 6,
- 0f, dbSnp);
- sf6.setValue("alleles", "T,C"); // TTT -> TTC synonymous
- sf6.setValue("ID", "var6");
-
- SequenceFeature sf7 = new SequenceFeature("sequence_variant", "", 8, 8,
- 0f, cosmic);
- sf7.setValue("alleles", "C,A,G"); // CCC -> CAC,CGC -> P/H/R
- sf7.setValue("ID", "var7");
- sf7.setValue("clinical_significance", "Good");
-
- List<DnaVariant> codon1Variants = new ArrayList<>();
- List<DnaVariant> codon2Variants = new ArrayList<>();
- List<DnaVariant> codon3Variants = new ArrayList<>();
- 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));
- codon1Variants.add(new DnaVariant("A", sf3));
- codon2Variants.add(new DnaVariant("A"));
- // codon2Variants.add(new DnaVariant("A"));
- codon3Variants.add(new DnaVariant("A", sf4));
- codon3Variants.add(new DnaVariant("A", sf5));
- 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", sf6));
- 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", sf7));
- codon3Variants.add(new DnaVariant("C"));
- AlignmentUtils.computePeptideVariants(peptide, 3, codonVariants);
-
- /*
- * verify added sequence features for
- * var1 K -> E Ensembl
- * var2 K -> Q dbSNP
- * var3 K -> stop
- * var4 synonymous
- * var5 K -> N Ensembl
- * var6 synonymous
- * var7 P -> H COSMIC
- * var8 P -> R COSMIC
- */
- List<SequenceFeature> sfs = peptide.getSequenceFeatures();
- SequenceFeatures.sortFeatures(sfs, true);
- assertEquals(8, sfs.size());
-
- /*
- * features are sorted by start position ascending, but in no
- * particular order where start positions match; asserts here
- * simply match the data returned (the order is not important)
- */
- // AAA -> AAT -> K/N
- SequenceFeature sf = sfs.get(0);
- assertEquals(1, sf.getBegin());
- assertEquals(1, sf.getEnd());
- assertEquals("nonsynonymous_variant", sf.getType());
- assertEquals("p.Lys1Asn", sf.getDescription());
- assertEquals("var5", sf.getValue("ID"));
- assertEquals("Benign", sf.getValue("clinical_significance"));
- assertEquals("ID=var5;clinical_significance=Benign",
- sf.getAttributes());
- assertEquals(1, sf.links.size());
- assertEquals(
- "p.Lys1Asn var5|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var5",
- sf.links.get(0));
- assertEquals(ensembl, sf.getFeatureGroup());
-
- // AAA -> CAA -> K/Q
- sf = sfs.get(1);
- assertEquals(1, sf.getBegin());
- assertEquals(1, sf.getEnd());
- assertEquals("nonsynonymous_variant", sf.getType());
- 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(dbSnp, sf.getFeatureGroup());
-
- // AAA -> GAA -> K/E
- sf = sfs.get(2);
- assertEquals(1, sf.getBegin());
- assertEquals(1, sf.getEnd());
- assertEquals("nonsynonymous_variant", sf.getType());
- 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(ensembl, sf.getFeatureGroup());
-
- // AAA -> TAA -> stop codon
- sf = sfs.get(3);
- assertEquals(1, sf.getBegin());
- assertEquals(1, sf.getEnd());
- assertEquals("stop_gained", sf.getType());
- assertEquals("Aaa/Taa", sf.getDescription());
- assertEquals("var3", sf.getValue("ID"));
- assertEquals("Bad", sf.getValue("clinical_significance"));
- assertEquals("ID=var3;clinical_significance=Bad", sf.getAttributes());
- assertEquals(1, sf.links.size());
- assertEquals(
- "Aaa/Taa var3|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var3",
- sf.links.get(0));
- assertEquals(dbSnp, sf.getFeatureGroup());
-
- // AAA -> AAG synonymous
- sf = sfs.get(4);
- assertEquals(1, sf.getBegin());
- assertEquals(1, sf.getEnd());
- assertEquals("synonymous_variant", sf.getType());
- assertEquals("aaA/aaG", sf.getDescription());
- assertEquals("var4", sf.getValue("ID"));
- assertEquals("None", sf.getValue("clinical_significance"));
- assertEquals("ID=var4;clinical_significance=None", sf.getAttributes());
- assertEquals(1, sf.links.size());
- assertEquals(
- "aaA/aaG var4|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var4",
- sf.links.get(0));
- assertEquals(cosmic, sf.getFeatureGroup());
-
- // TTT -> TTC synonymous
- sf = sfs.get(5);
- assertEquals(2, sf.getBegin());
- assertEquals(2, sf.getEnd());
- assertEquals("synonymous_variant", sf.getType());
- assertEquals("ttT/ttC", sf.getDescription());
- assertEquals("var6", sf.getValue("ID"));
- assertNull(sf.getValue("clinical_significance"));
- assertEquals("ID=var6", sf.getAttributes());
- assertEquals(1, sf.links.size());
- assertEquals(
- "ttT/ttC var6|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var6",
- sf.links.get(0));
- assertEquals(dbSnp, sf.getFeatureGroup());
-
- // var7 generates two distinct protein variant features (two alleles)
- // CCC -> CGC -> P/R
- sf = sfs.get(6);
- assertEquals(3, sf.getBegin());
- assertEquals(3, sf.getEnd());
- assertEquals("nonsynonymous_variant", sf.getType());
- assertEquals("p.Pro3Arg", sf.getDescription());
- assertEquals("var7", sf.getValue("ID"));
- assertEquals("Good", sf.getValue("clinical_significance"));
- assertEquals("ID=var7;clinical_significance=Good", sf.getAttributes());
- assertEquals(1, sf.links.size());
- assertEquals(
- "p.Pro3Arg var7|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var7",
- sf.links.get(0));
- assertEquals(cosmic, sf.getFeatureGroup());
-
- // CCC -> CAC -> P/H
- sf = sfs.get(7);
- assertEquals(3, sf.getBegin());
- assertEquals(3, sf.getEnd());
- assertEquals("nonsynonymous_variant", sf.getType());
- assertEquals("p.Pro3His", sf.getDescription());
- assertEquals("var7", sf.getValue("ID"));
- assertEquals("Good", sf.getValue("clinical_significance"));
- assertEquals("ID=var7;clinical_significance=Good", sf.getAttributes());
- assertEquals(1, sf.links.size());
- assertEquals(
- "p.Pro3His var7|http://www.ensembl.org/Homo_sapiens/Variation/Summary?v=var7",
- sf.links.get(0));
- assertEquals(cosmic, sf.getFeatureGroup());
- }
-
- /**
* Tests for the method that maps the subset of a dna sequence that has CDS
* (or subtype) feature, with CDS strand = '-' (reverse)
*/
AlignmentI al2 = new Alignment(new SequenceI[] { dna3, dna4 });
((Alignment) al2).createDatasetAlignment();
+ /*
+ * alignment removes gapped columns (two internal, two trailing)
+ */
assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
- assertEquals(seq1, al1.getSequenceAt(0).getSequenceAsString());
- assertEquals(seq2, al1.getSequenceAt(1).getSequenceAsString());
+ String aligned1 = "-cc-GG-GTTT-aaa";
+ assertEquals(aligned1,
+ al1.getSequenceAt(0).getSequenceAsString());
+ String aligned2 = "C--C-Cgg-gtttAAA";
+ assertEquals(aligned2,
+ al1.getSequenceAt(1).getSequenceAsString());
/*
* add another sequence to 'aligned' - should still succeed, since
dna5.createDatasetSequence();
al2.addSequence(dna5);
assertTrue(AlignmentUtils.alignAsSameSequences(al1, al2));
- assertEquals(seq1, al1.getSequenceAt(0).getSequenceAsString());
- assertEquals(seq2, al1.getSequenceAt(1).getSequenceAsString());
+ assertEquals(aligned1, al1.getSequenceAt(0).getSequenceAsString());
+ assertEquals(aligned2, al1.getSequenceAt(1).getSequenceAsString());
/*
* add another sequence to 'unaligned' - should fail, since now not
{
SequenceI dna1 = new Sequence("dna1", "cccGGGTTTaaa");
SequenceI dna2 = new Sequence("dna2", "CCCgggtttAAA");
- SequenceI as1 = dna1.deriveSequence();
- SequenceI as2 = dna1.deriveSequence().getSubSequence(3, 7);
- SequenceI as3 = dna2.deriveSequence();
+ SequenceI as1 = dna1.deriveSequence(); // cccGGGTTTaaa/1-12
+ SequenceI as2 = dna1.deriveSequence().getSubSequence(3, 7); // GGGT/4-7
+ SequenceI as3 = dna2.deriveSequence(); // CCCgggtttAAA/1-12
as1.insertCharAt(6, 5, '-');
- String s_as1 = as1.getSequenceAsString();
+ assertEquals("cccGGG-----TTTaaa", as1.getSequenceAsString());
as2.insertCharAt(6, 5, '-');
- String s_as2 = as2.getSequenceAsString();
- as3.insertCharAt(6, 5, '-');
- String s_as3 = as3.getSequenceAsString();
+ assertEquals("GGGT-----", as2.getSequenceAsString());
+ as3.insertCharAt(3, 5, '-');
+ assertEquals("CCC-----gggtttAAA", as3.getSequenceAsString());
AlignmentI aligned = new Alignment(new SequenceI[] { as1, as2, as3 });
// why do we need to cast this still ?
uas3 });
((Alignment) tobealigned).createDatasetAlignment();
+ /*
+ * alignAs lines up dataset sequences and removes empty columns (two)
+ */
assertTrue(AlignmentUtils.alignAsSameSequences(tobealigned, aligned));
- assertEquals(s_as1, uas1.getSequenceAsString());
- assertEquals(s_as2, uas2.getSequenceAsString());
- assertEquals(s_as3, uas3.getSequenceAsString());
+ assertEquals("cccGGG---TTTaaa", uas1.getSequenceAsString());
+ assertEquals("GGGT", uas2.getSequenceAsString());
+ assertEquals("CCC---gggtttAAA", uas3.getSequenceAsString());
}
@Test(groups = { "Functional" })
* transcript 'CDS' is 10-16, 17-21
* which is 'gene' 158-164, 210-214
*/
- MapList toMap = toLoci.getMap();
+ MapList toMap = toLoci.getMapping();
assertEquals(1, toMap.getFromRanges().size());
assertEquals(2, toMap.getFromRanges().get(0).length);
assertEquals(1, toMap.getFromRanges().get(0)[0]);
assertEquals(12, toMap.getFromRanges().get(0)[1]);
- assertEquals(1, toMap.getToRanges().size());
- assertEquals(4, toMap.getToRanges().get(0).length);
+ assertEquals(2, toMap.getToRanges().size());
+ assertEquals(2, toMap.getToRanges().get(0).length);
assertEquals(158, toMap.getToRanges().get(0)[0]);
assertEquals(164, toMap.getToRanges().get(0)[1]);
- assertEquals(210, toMap.getToRanges().get(0)[2]);
- assertEquals(214, toMap.getToRanges().get(0)[3]);
+ assertEquals(210, toMap.getToRanges().get(1)[0]);
+ assertEquals(214, toMap.getToRanges().get(1)[1]);
// or summarised as (but toString might change in future):
- assertEquals("[ [1, 12] ] 1:1 to [ [158, 164, 210, 214] ]",
+ assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]",
toMap.toString());
/*
AlignmentUtils.transferGeneLoci(from, map, to);
assertEquals("GRCh38", toLoci.getAssemblyId());
assertEquals("7", toLoci.getChromosomeId());
- toMap = toLoci.getMap();
- assertEquals("[ [1, 12] ] 1:1 to [ [158, 164, 210, 214] ]",
+ toMap = toLoci.getMapping();
+ assertEquals("[ [1, 12] ] 1:1 to [ [158, 164] [210, 214] ]",
toMap.toString());
}
* Case 2: CDS 3 times length of peptide + stop codon
* (note code does not currently check trailing codon is a stop codon)
*/
- dna = new Sequence("dna", "AACGacgtCTCCTTGA");
+ dna = new Sequence("dna", "AACGacgtCTCCTCCC");
dna.createDatasetSequence();
dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 16, null));
Arrays.deepToString(ml.getFromRanges().toArray()));
/*
- * Case 3: CDS not 3 times length of peptide - no mapping is made
+ * Case 3: CDS longer than 3 * peptide + stop codon - no mapping is made
+ */
+ dna = new Sequence("dna", "AACGacgtCTCCTTGATCA");
+ dna.createDatasetSequence();
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 19, null));
+ ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
+ assertNull(ml);
+
+ /*
+ * Case 4: CDS shorter than 3 * peptide - no mapping is made
+ */
+ dna = new Sequence("dna", "AACGacgtCTCC");
+ dna.createDatasetSequence();
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
+ dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 12, null));
+ ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
+ assertNull(ml);
+
+ /*
+ * Case 5: CDS 3 times length of peptide + part codon - mapping is truncated
*/
dna = new Sequence("dna", "AACGacgtCTCCTTG");
dna.createDatasetSequence();
dna.addSequenceFeature(new SequenceFeature("CDS", "", 1, 4, null));
dna.addSequenceFeature(new SequenceFeature("CDS", "", 9, 15, null));
ml = AlignmentUtils.mapCdsToProtein(dna, peptide);
- assertNull(ml);
+ assertEquals(3, ml.getFromRatio());
+ assertEquals(1, ml.getToRatio());
+ assertEquals("[[1, 3]]",
+ Arrays.deepToString(ml.getToRanges().toArray()));
+ assertEquals("[[1, 4], [9, 13]]",
+ Arrays.deepToString(ml.getFromRanges().toArray()));
/*
- * Case 4: incomplete start codon corresponding to X in peptide
+ * Case 6: incomplete start codon corresponding to X in peptide
*/
dna = new Sequence("dna", "ACGacgtCTCCTTGG");
dna.createDatasetSequence();
assertEquals("[[3, 3], [8, 12]]",
Arrays.deepToString(ml.getFromRanges().toArray()));
}
+
+ /**
+ * Tests for the method that locates the CDS sequence that has a mapping to
+ * the given protein. That is, given a transcript-to-peptide mapping, find the
+ * cds-to-peptide mapping that relates to both, and return the CDS sequence.
+ */
+ @Test
+ public void testFindCdsForProtein()
+ {
+ List<AlignedCodonFrame> mappings = new ArrayList<>();
+ AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ mappings.add(acf1);
+
+ SequenceI dna1 = new Sequence("dna1", "cgatATcgGCTATCTATGacg");
+ dna1.createDatasetSequence();
+
+ // NB we currently exclude STOP codon from CDS sequences
+ // the test would need to change if this changes in future
+ SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
+ cds1.createDatasetSequence();
+
+ SequenceI pep1 = new Sequence("pep1", "MLS");
+ pep1.createDatasetSequence();
+ List<AlignedCodonFrame> seqMappings = new ArrayList<>();
+ MapList mapList = new MapList(
+ new int[]
+ { 5, 6, 9, 15 }, new int[] { 1, 3 }, 3, 1);
+ Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList);
+
+ // add dna to peptide mapping
+ seqMappings.add(acf1);
+ acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
+ mapList);
+
+ /*
+ * first case - no dna-to-CDS mapping exists - search fails
+ */
+ SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
+ seqMappings, dnaToPeptide);
+ assertNull(seq);
+
+ /*
+ * second case - CDS-to-peptide mapping exists but no dna-to-CDS
+ * - search fails
+ */
+ // todo this test fails if the mapping is added to acf1, not acf2
+ // need to tidy up use of lists of mappings in AlignedCodonFrame
+ AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ mappings.add(acf2);
+ MapList cdsToPeptideMapping = new MapList(new int[]
+ { 1, 9 }, new int[] { 1, 3 }, 3, 1);
+ acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
+ cdsToPeptideMapping);
+ assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
+ dnaToPeptide));
+
+ /*
+ * third case - add dna-to-CDS mapping - CDS is now found!
+ */
+ MapList dnaToCdsMapping = new MapList(new int[] { 5, 6, 9, 15 },
+ new int[]
+ { 1, 9 }, 1, 1);
+ acf1.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(),
+ dnaToCdsMapping);
+ seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
+ dnaToPeptide);
+ assertSame(seq, cds1.getDatasetSequence());
+ }
+
+ /**
+ * Tests for the method that locates the CDS sequence that has a mapping to
+ * the given protein. That is, given a transcript-to-peptide mapping, find the
+ * cds-to-peptide mapping that relates to both, and return the CDS sequence.
+ * This test is for the case where transcript and CDS are the same length.
+ */
+ @Test
+ public void testFindCdsForProtein_noUTR()
+ {
+ List<AlignedCodonFrame> mappings = new ArrayList<>();
+ AlignedCodonFrame acf1 = new AlignedCodonFrame();
+ mappings.add(acf1);
+
+ SequenceI dna1 = new Sequence("dna1", "ATGCTATCTTAA");
+ dna1.createDatasetSequence();
+
+ // NB we currently exclude STOP codon from CDS sequences
+ // the test would need to change if this changes in future
+ SequenceI cds1 = new Sequence("cds1", "ATGCTATCT");
+ cds1.createDatasetSequence();
+
+ SequenceI pep1 = new Sequence("pep1", "MLS");
+ pep1.createDatasetSequence();
+ List<AlignedCodonFrame> seqMappings = new ArrayList<>();
+ MapList mapList = new MapList(
+ new int[]
+ { 1, 9 }, new int[] { 1, 3 }, 3, 1);
+ Mapping dnaToPeptide = new Mapping(pep1.getDatasetSequence(), mapList);
+
+ // add dna to peptide mapping
+ seqMappings.add(acf1);
+ acf1.addMap(dna1.getDatasetSequence(), pep1.getDatasetSequence(),
+ mapList);
+
+ /*
+ * first case - transcript lacks CDS features - it appears to be
+ * the CDS sequence and is returned
+ */
+ SequenceI seq = AlignmentUtils.findCdsForProtein(mappings, dna1,
+ seqMappings, dnaToPeptide);
+ assertSame(seq, dna1.getDatasetSequence());
+
+ /*
+ * second case - transcript has CDS feature - this means it is
+ * not returned as a match for CDS (CDS sequences don't have CDS features)
+ */
+ dna1.addSequenceFeature(
+ new SequenceFeature(SequenceOntologyI.CDS, "cds", 1, 12, null));
+ seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
+ dnaToPeptide);
+ assertNull(seq);
+
+ /*
+ * third case - CDS-to-peptide mapping exists but no dna-to-CDS
+ * - search fails
+ */
+ // todo this test fails if the mapping is added to acf1, not acf2
+ // need to tidy up use of lists of mappings in AlignedCodonFrame
+ AlignedCodonFrame acf2 = new AlignedCodonFrame();
+ mappings.add(acf2);
+ MapList cdsToPeptideMapping = new MapList(new int[]
+ { 1, 9 }, new int[] { 1, 3 }, 3, 1);
+ acf2.addMap(cds1.getDatasetSequence(), pep1.getDatasetSequence(),
+ cdsToPeptideMapping);
+ assertNull(AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
+ dnaToPeptide));
+
+ /*
+ * fourth case - add dna-to-CDS mapping - CDS is now found!
+ */
+ MapList dnaToCdsMapping = new MapList(new int[] { 1, 9 },
+ new int[]
+ { 1, 9 }, 1, 1);
+ acf1.addMap(dna1.getDatasetSequence(), cds1.getDatasetSequence(),
+ dnaToCdsMapping);
+ seq = AlignmentUtils.findCdsForProtein(mappings, dna1, seqMappings,
+ dnaToPeptide);
+ assertSame(seq, cds1.getDatasetSequence());
+ }
}
git://source.jalview.org / jalview.git / blobdiff