transcriptRange = Arrays
+ .asList(new int[]
+ { transcript.getStart(), transcript.getEnd() });
+ MapList mapList = new MapList(transcriptRange, transcriptLoci, 1, 1);
+
+ transcript.setGeneLoci(loci.getSpeciesId(), loci.getAssemblyId(),
+ loci.getChromosomeId(), mapList);
+ }
+
+ /**
+ * Returns the 'transcript_id' property of the sequence feature (or null)
+ *
+ * @param feature
+ * @return
+ */
+ protected String getTranscriptId(SequenceFeature feature)
+ {
+ return (String) feature.getValue(JSON_ID);
+ }
+
+ /**
+ * Returns a list of the transcript features on the sequence whose Parent is
+ * the gene for the accession id.
+ *
+ * Transcript features are those of type "transcript", or any of its sub-types
+ * in the Sequence Ontology e.g. "mRNA", "processed_transcript". We also
+ * include "NMD_transcript_variant", because this type behaves like a
+ * transcript identifier in Ensembl, although strictly speaking it is not in
+ * the SO.
+ *
+ * @param accId
+ * @param geneSequence
+ * @return
+ */
+ protected List getTranscriptFeatures(String accId,
+ SequenceI geneSequence)
+ {
+ List transcriptFeatures = new ArrayList<>();
+
+ String parentIdentifier = accId;
+
+ List sfs = geneSequence.getFeatures()
+ .getFeaturesByOntology(SequenceOntologyI.TRANSCRIPT);
+ sfs.addAll(geneSequence.getFeatures().getPositionalFeatures(
+ SequenceOntologyI.NMD_TRANSCRIPT_VARIANT));
+
+ for (SequenceFeature sf : sfs)
{
- geneSequence.getDatasetSequence().setSequenceFeatures(
- keptFeatures.toArray(new SequenceFeature[keptFeatures
- .size()]));
+ String parent = (String) sf.getValue(PARENT);
+ if (parentIdentifier.equalsIgnoreCase(parent))
+ {
+ transcriptFeatures.add(sf);
+ }
}
- return transcriptIds;
+
+ return transcriptFeatures;
}
@Override
public String getDescription()
{
- return "Fetches all transcripts and variant features for a gene";
+ return "Fetches all transcripts and variant features for a gene or transcript";
}
/**
- * Default test query is a transcript
+ * Default test query is a gene id (can also enter a transcript id)
*/
@Override
public String getTestQuery()
{
- return "ENSG00000157764"; // reverse strand
- // ENSG00000090266 // forward strand
+ return Platform.isJS() ? "ENSG00000123569" : "ENSG00000157764";
+ // ENSG00000123569 // H2BFWT histone, 2 transcripts, reverse strand
+ // ENSG00000157764 // BRAF, 5 transcripts, reverse strand
+ // ENSG00000090266 // NDUFB2, 15 transcripts, forward strand
+ // ENSG00000101812 // H2BFM histone, 3 transcripts, forward strand
}
/**
- * Answers true for a feature of type 'gene' (or a sub-type of gene in the
- * Sequence Ontology), whose ID is the accession we are retrieving
+ * Answers a list of sequence features (if any) whose type is 'gene' (or a
+ * subtype of gene in the Sequence Ontology), and whose ID is the accession we
+ * are retrieving
*/
@Override
- protected boolean identifiesSequence(SequenceFeature sf, String accId)
+ protected List getIdentifyingFeatures(SequenceI seq,
+ String accId)
{
- if (SequenceOntology.getInstance().isA(sf.getType(),
- SequenceOntology.GENE))
+ List result = new ArrayList<>();
+ List sfs = seq.getFeatures()
+ .getFeaturesByOntology(SequenceOntologyI.GENE);
+ for (SequenceFeature sf : sfs)
{
- String id = (String) sf.getValue(ID);
- if (("gene:" + accId).equals(id))
+ String id = (String) sf.getValue(JSON_ID);
+ if (accId.equalsIgnoreCase(id))
{
- return true;
+ result.add(sf);
}
}
- return false;
+ return result;
}
/**
- * Answers true unless feature type is 'gene'. We need the gene features to
- * identify the range, but it is redundant information on the gene sequence.
+ * Answers true unless feature type is 'gene', or 'transcript' with a parent
+ * which is a different gene. We need the gene features to identify the range,
+ * but it is redundant information on the gene sequence. Checking the parent
+ * allows us to drop transcript features which belong to different
+ * (overlapping) genes.
*/
@Override
protected boolean retainFeature(SequenceFeature sf, String accessionId)
{
- return !SequenceOntology.getInstance().isA(sf.getType(),
- SequenceOntology.GENE);
+ SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+ String type = sf.getType();
+ if (so.isA(type, SequenceOntologyI.GENE))
+ {
+ return false;
+ }
+ if (isTranscript(type))
+ {
+ String parent = (String) sf.getValue(PARENT);
+ if (!accessionId.equalsIgnoreCase(parent))
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ * Override to do nothing as Ensembl doesn't return a protein sequence for a
+ * gene identifier
+ */
+ @Override
+ protected void addProteinProduct(SequenceI querySeq)
+ {
+ }
+
+ @Override
+ public Regex getAccessionValidator()
+ {
+ return ACCESSION_REGEX;
+ }
+
+ /**
+ * Returns a descriptor for suitable feature display settings with
+ *
+ * - only exon or sequence_variant features (or their subtypes in the
+ * Sequence Ontology) visible
+ * - variant features coloured red
+ * - exon features coloured by label (exon name)
+ * - variants displayed above (on top of) exons
+ *
+ */
+ @Override
+ public FeatureSettingsModelI getFeatureColourScheme()
+ {
+ return new FeatureSettingsAdapter()
+ {
+ SequenceOntologyI so = SequenceOntologyFactory.getInstance();
+
+ @Override
+ public boolean isFeatureHidden(String type)
+ {
+ return (!so.isA(type, SequenceOntologyI.EXON)
+ && !so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT));
+ }
+
+ @Override
+ public FeatureColourI getFeatureColour(String type)
+ {
+ if (so.isA(type, SequenceOntologyI.EXON))
+ {
+ return new FeatureColour()
+ {
+ @Override
+ public boolean isColourByLabel()
+ {
+ return true;
+ }
+ };
+ }
+ if (so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT))
+ {
+ return new FeatureColour()
+ {
+
+ @Override
+ public Color getColour()
+ {
+ return Color.RED;
+ }
+ };
+ }
+ return null;
+ }
+
+ /**
+ * order to render sequence_variant after exon after the rest
+ */
+ @Override
+ public int compare(String feature1, String feature2)
+ {
+ if (so.isA(feature1, SequenceOntologyI.SEQUENCE_VARIANT))
+ {
+ return +1;
+ }
+ if (so.isA(feature2, SequenceOntologyI.SEQUENCE_VARIANT))
+ {
+ return -1;
+ }
+ if (so.isA(feature1, SequenceOntologyI.EXON))
+ {
+ return +1;
+ }
+ if (so.isA(feature2, SequenceOntologyI.EXON))
+ {
+ return -1;
+ }
+ return 0;
+ }
+ };
}
}