import jalview.datamodel.Mapping;
import jalview.datamodel.SearchResults;
import jalview.datamodel.Sequence;
-import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceGroup;
import jalview.datamodel.SequenceI;
import jalview.schemes.ResidueProperties;
final SequenceI ds = dnaSeq.getDatasetSequence();
List<AlignedCodonFrame> seqMappings = MappingUtils
.findMappingsForSequence(ds, mappings);
- if (!seqMappings.isEmpty())
+ for (AlignedCodonFrame acf : seqMappings)
{
- /*
- * We assume here that only one protein mapping is expected per dna
- * sequence. Mapping to multiple protein sequences is conceivable but
- * undefined. Splitting a mapping to one protein sequence across
- * multiple mappings is possible but pathological. Need closer
- * constraints on the contents of AlignedCodonFrame.
- */
AlignedCodonFrame newMapping = new AlignedCodonFrame();
- final SequenceI exonSequence = makeExonSequence(ds,
- seqMappings.get(0), newMapping);
- exonSequences.add(exonSequence);
- newMappings.add(newMapping);
+ final List<SequenceI> mappedExons = makeExonSequences(ds, acf,
+ newMapping);
+ if (!mappedExons.isEmpty())
+ {
+ exonSequences.addAll(mappedExons);
+ newMappings.add(newMapping);
+ }
}
}
AlignmentI al = new Alignment(
}
/**
- * Helper method to make an exon-only sequence and populate its mapping to
- * protein
+ * Helper method to make exon-only sequences and populate their mappings to
+ * protein products
* <p>
* For example, if ggCCaTTcGAg has mappings [3, 4, 6, 7, 9, 10] to protein
* then generate a sequence CCTTGA with mapping [1, 6] to the same protein
* residues
+ * <p>
+ * Typically eukaryotic dna will include exons encoding for a single peptide
+ * sequence i.e. return a single result. Bacterial dna may have overlapping
+ * exon mappings coding for multiple peptides so return multiple results
+ * (example EMBL KF591215).
*
* @param dnaSeq
* a dna dataset sequence
* @param mapping
- * the current mapping of the sequence to protein
+ * containing one or more mappings of the sequence to protein
* @param newMapping
- * the new mapping to populate, from the exon-only sequence
+ * the new mapping to populate, from the exon-only sequences to their
+ * mapped protein sequences
* @return
*/
- protected static SequenceI makeExonSequence(SequenceI dnaSeq,
- AlignedCodonFrame acf, AlignedCodonFrame newMapping)
+ protected static List<SequenceI> makeExonSequences(SequenceI dnaSeq,
+ AlignedCodonFrame mapping, AlignedCodonFrame newMapping)
{
- Mapping mapping = acf.getMappingForSequence(dnaSeq);
+ List<SequenceI> exonSequences = new ArrayList<SequenceI>();
+ List<Mapping> seqMappings = mapping.getMappingsForSequence(dnaSeq);
final char[] dna = dnaSeq.getSequence();
- StringBuilder newSequence = new StringBuilder(dnaSeq.getLength());
-
- /*
- * Get the codon regions as { [2, 5], [7, 12], [14, 14] etc }
- */
- List<int[]> exonRanges = mapping.getMap().getFromRanges();
- for (int[] range : exonRanges)
+ for (Mapping seqMapping : seqMappings)
{
- for (int pos = range[0]; pos <= range[1]; pos++)
+ StringBuilder newSequence = new StringBuilder(dnaSeq.getLength());
+
+ /*
+ * Get the codon regions as { [2, 5], [7, 12], [14, 14] etc }
+ */
+ List<int[]> exonRanges = seqMapping.getMap().getFromRanges();
+ for (int[] range : exonRanges)
{
- newSequence.append(dna[pos - 1]);
+ for (int pos = range[0]; pos <= range[1]; pos++)
+ {
+ newSequence.append(dna[pos - 1]);
+ }
}
- }
- SequenceI exon = new Sequence(dnaSeq.getName(), newSequence.toString());
+ SequenceI exon = new Sequence(dnaSeq.getName(),
+ newSequence.toString());
- /*
- * Locate any xrefs to CDS database on the protein product and attach to the
- * CDS sequence. Also add as a sub-token of the sequence name.
- */
- // default to "CDS" if we can't locate an actual gene id
- String cdsAccId = FeatureProperties.getCodingFeature(DBRefSource.EMBL);
- DBRefEntry[] cdsRefs = DBRefUtils.selectRefs(
- mapping.getTo().getDBRef(), DBRefSource.CODINGDBS);
- if (cdsRefs != null)
- {
- for (DBRefEntry cdsRef : cdsRefs)
+ /*
+ * Locate any xrefs to CDS database on the protein product and attach to
+ * the CDS sequence. Also add as a sub-token of the sequence name.
+ */
+ // default to "CDS" if we can't locate an actual gene id
+ String cdsAccId = FeatureProperties
+ .getCodingFeature(DBRefSource.EMBL);
+ DBRefEntry[] cdsRefs = DBRefUtils.selectRefs(seqMapping.getTo()
+ .getDBRef(), DBRefSource.CODINGDBS);
+ if (cdsRefs != null)
{
- exon.addDBRef(new DBRefEntry(cdsRef));
- cdsAccId = cdsRef.getAccessionId();
+ for (DBRefEntry cdsRef : cdsRefs)
+ {
+ exon.addDBRef(new DBRefEntry(cdsRef));
+ cdsAccId = cdsRef.getAccessionId();
+ }
}
- }
- exon.setName(exon.getName() + "|" + cdsAccId);
- exon.createDatasetSequence();
+ exon.setName(exon.getName() + "|" + cdsAccId);
+ exon.createDatasetSequence();
- /*
- * Build new mappings - from the same protein regions, but now to contiguous
- * exons
- */
- List<int[]> exonRange = new ArrayList<int[]>();
- exonRange.add(new int[]
- { 1, newSequence.length() });
- MapList map = new MapList(exonRange, mapping.getMap().getToRanges(), 3, 1);
- newMapping.addMap(exon.getDatasetSequence(), mapping.getTo(), map);
+ /*
+ * Build new mappings - from the same protein regions, but now to
+ * contiguous exons
+ */
+ List<int[]> exonRange = new ArrayList<int[]>();
+ exonRange.add(new int[]
+ { 1, newSequence.length() });
+ MapList map = new MapList(exonRange, seqMapping.getMap()
+ .getToRanges(),
+ 3, 1);
+ newMapping.addMap(exon.getDatasetSequence(), seqMapping.getTo(), map);
- return exon;
+ exonSequences.add(exon);
+ }
+ return exonSequences;
}
}
*/
package jalview.datamodel;
+import java.util.ArrayList;
+import java.util.List;
+
import jalview.util.MapList;
import jalview.util.MappingUtils;
{ dnaSeq[codonPos[0] - 1], dnaSeq[codonPos[1] - 1],
dnaSeq[codonPos[2] - 1] };
}
+
+ /**
+ * Returns any mappings found which are to (or from) the given sequence, and
+ * to distinct sequences.
+ *
+ * @param seq
+ * @return
+ */
+ public List<Mapping> getMappingsForSequence(SequenceI seq)
+ {
+ List<Mapping> result = new ArrayList<Mapping>();
+ if (dnaSeqs == null)
+ {
+ return result;
+ }
+ List<SequenceI> related = new ArrayList<SequenceI>();
+ SequenceI seqDs = seq.getDatasetSequence();
+ seqDs = seqDs != null ? seqDs : seq;
+
+ for (int ds = 0; ds < dnaSeqs.length; ds++)
+ {
+ final Mapping mapping = dnaToProt[ds];
+ if (dnaSeqs[ds] == seqDs || mapping.to == seqDs)
+ {
+ if (!related.contains(mapping.to))
+ {
+ result.add(mapping);
+ related.add(mapping.to);
+ }
+ }
+ }
+ return result;
+ }
}
import java.util.Arrays;
import java.util.Collections;
import java.util.HashSet;
+import java.util.LinkedHashSet;
import java.util.List;
import java.util.Map;
import java.util.Set;
* x-ref to the EMBLCDS record.
*/
@Test
- public void testMakeExonSequence()
+ public void testMakeExonSequences()
{
SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
SequenceI pep1 = new Sequence("pep1", "GF");
mappings.add(acf);
AlignedCodonFrame newMapping = new AlignedCodonFrame();
- SequenceI exon = AlignmentUtils.makeExonSequence(dna1, acf, newMapping);
+ 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("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
+ public void testMakeExonAlignment_multipleProteins()
+ {
+ SequenceI dna1 = new Sequence("dna1", "aaaGGGcccTTTaaa");
+ SequenceI pep1 = new Sequence("pep1", "GF"); // GGGTTT
+ SequenceI pep2 = new Sequence("pep2", "KP"); // aaaccc
+ SequenceI pep3 = new Sequence("pep3", "KF"); // aaaTTT
+ dna1.createDatasetSequence();
+ pep1.createDatasetSequence();
+ pep2.createDatasetSequence();
+ pep3.createDatasetSequence();
+ pep1.getDatasetSequence().addDBRef(
+ new DBRefEntry("EMBLCDS", "2", "A12345"));
+ pep2.getDatasetSequence().addDBRef(
+ new DBRefEntry("EMBLCDS", "3", "A12346"));
+ pep3.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.
+ */
+ Set<AlignedCodonFrame> mappings = new LinkedHashSet<AlignedCodonFrame>();
+ // map ...GGG...TTT to GF
+ 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);
+
+ // map aaa...ccc to KP
+ map = new MapList(new int[]
+ { 1, 3, 7, 9 }, new int[]
+ { 1, 2 }, 3, 1);
+ acf = new AlignedCodonFrame();
+ acf.addMap(dna1.getDatasetSequence(), pep2.getDatasetSequence(), map);
+ mappings.add(acf);
+
+ // map aaa......TTT to KF
+ map = new MapList(new int[]
+ { 1, 3, 10, 12 }, new int[]
+ { 1, 2 }, 3, 1);
+ acf = new AlignedCodonFrame();
+ acf.addMap(dna1.getDatasetSequence(), pep3.getDatasetSequence(), map);
+ mappings.add(acf);
+
+ AlignmentI exal = AlignmentUtils.makeExonAlignment(new SequenceI[]
+ { dna1 }, mappings);
+
+ /*
+ * Verify we have 3 exon sequences, mapped to pep1/2/3 respectively
+ */
+ List<SequenceI> exons = exal.getSequences();
+ assertEquals(3, 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());
+
+ 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());
+ 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());
}
}
git://source.jalview.org / jalview.git / commitdiff