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package jalview.ext.ensembl; |
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import jalview.api.FeatureColourI; |
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import jalview.api.FeatureSettingsModelI; |
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import jalview.datamodel.AlignmentI; |
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import jalview.datamodel.GeneLociI; |
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import jalview.datamodel.Sequence; |
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import jalview.datamodel.SequenceFeature; |
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import jalview.datamodel.SequenceI; |
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import jalview.datamodel.features.SequenceFeatures; |
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import jalview.io.gff.SequenceOntologyFactory; |
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import jalview.io.gff.SequenceOntologyI; |
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import jalview.schemes.FeatureColour; |
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import jalview.schemes.FeatureSettingsAdapter; |
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import jalview.util.MapList; |
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import jalview.util.Platform; |
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import java.awt.Color; |
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import java.io.UnsupportedEncodingException; |
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import java.net.URLDecoder; |
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import java.util.ArrayList; |
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import java.util.Arrays; |
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import java.util.List; |
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import com.stevesoft.pat.Regex; |
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@author |
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| 29.4% |
Uncovered Elements: 173 (245) |
Complexity: 59 |
Complexity Density: 0.37 |
|
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public class EnsemblGene extends EnsemblSeqProxy |
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{ |
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private static final Regex ACCESSION_REGEX = new Regex(".*"); |
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private static final EnsemblFeatureType[] FEATURES_TO_FETCH = { |
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EnsemblFeatureType.gene, EnsemblFeatureType.transcript, |
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EnsemblFeatureType.exon, EnsemblFeatureType.cds, |
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EnsemblFeatureType.variation }; |
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private static final String CHROMOSOME = "chromosome"; |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public EnsemblGene()... |
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{ |
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super(); |
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} |
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@param |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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public EnsemblGene(String d)... |
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{ |
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super(d); |
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} |
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| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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3461 |
@Override... |
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public String getDbName() |
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{ |
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return "ENSEMBL"; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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@Override... |
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protected EnsemblFeatureType[] getFeaturesToFetch() |
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{ |
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return FEATURES_TO_FETCH; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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@Override... |
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protected EnsemblSeqType getSourceEnsemblType() |
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{ |
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return EnsemblSeqType.GENOMIC; |
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} |
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| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
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@Override... |
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protected String getObjectType() |
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{ |
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return OBJECT_TYPE_GENE; |
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} |
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@param |
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@return |
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| 0% |
Uncovered Elements: 20 (20) |
Complexity: 4 |
Complexity Density: 0.29 |
|
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@Override... |
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public AlignmentI getSequenceRecords(String query) throws Exception |
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{ |
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List<String> geneIds = getGeneIds(query); |
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AlignmentI al = null; |
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for (String geneId : geneIds) |
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{ |
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AlignmentI geneAlignment = super.getSequenceRecords(geneId); |
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if (geneAlignment == null) |
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{ |
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continue; |
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} |
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if (geneAlignment.getHeight() == 1) |
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{ |
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geneId = geneAlignment.getSequenceAt(0).getName(); |
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findGeneLoci(geneAlignment.getSequenceAt(0), geneId); |
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getTranscripts(geneAlignment, geneId); |
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} |
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if (al == null) |
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{ |
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al = geneAlignment; |
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} |
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else |
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{ |
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al.append(geneAlignment); |
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} |
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} |
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return al; |
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} |
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@param |
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@param |
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| 0% |
Uncovered Elements: 6 (6) |
Complexity: 2 |
Complexity Density: 0.5 |
|
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void findGeneLoci(SequenceI seq, String geneId)... |
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{ |
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GeneLociI geneLoci = new EnsemblLookup(getDomain()).getGeneLoci(geneId); |
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if (geneLoci != null) |
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{ |
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seq.setGeneLoci(geneLoci.getSpeciesId(), geneLoci.getAssemblyId(), |
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geneLoci.getChromosomeId(), geneLoci.getMapping()); |
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} |
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else |
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{ |
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parseChromosomeLocations(seq); |
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} |
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} |
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@param |
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| 0% |
Uncovered Elements: 27 (27) |
Complexity: 7 |
Complexity Density: 0.37 |
|
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boolean parseChromosomeLocations(SequenceI seq)... |
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{ |
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String description = seq.getDescription(); |
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if (description == null) |
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{ |
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return false; |
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} |
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String[] tokens = description.split(":"); |
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if (tokens.length == 6 && tokens[0].startsWith(CHROMOSOME)) |
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{ |
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String ref = tokens[1]; |
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String chrom = tokens[2]; |
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try |
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{ |
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int chStart = Integer.parseInt(tokens[3]); |
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int chEnd = Integer.parseInt(tokens[4]); |
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boolean forwardStrand = "1".equals(tokens[5]); |
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String species = ""; |
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int[] from = new int[] { seq.getStart(), seq.getEnd() }; |
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int[] to = new int[] { forwardStrand ? chStart : chEnd, |
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forwardStrand ? chEnd : chStart }; |
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MapList map = new MapList(from, to, 1, 1); |
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seq.setGeneLoci(species, ref, chrom, map); |
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return true; |
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} catch (NumberFormatException e) |
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{ |
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jalview.bin.Console |
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.errPrintln("Bad integers in description " + description); |
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} |
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} |
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return false; |
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} |
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@param |
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@return |
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| 0% |
Uncovered Elements: 17 (17) |
Complexity: 4 |
Complexity Density: 0.36 |
|
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List<String> getGeneIds(String accessions)... |
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{ |
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List<String> geneIds = new ArrayList<>(); |
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for (String acc : accessions.split(getAccessionSeparator())) |
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{ |
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String geneId = new EnsemblLookup(getDomain()).getGeneId(acc); |
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if (geneId != null) |
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{ |
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0 |
if (!geneIds.contains(geneId)) |
257 |
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{ |
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geneIds.add(geneId); |
259 |
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} |
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} |
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else |
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{ |
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List<String> ids = new EnsemblSymbol(getDomain(), getDbSource(), |
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getDbVersion()).getGeneIds(acc); |
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for (String id : ids) |
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{ |
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if (!geneIds.contains(id)) |
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{ |
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geneIds.add(id); |
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} |
275 |
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} |
276 |
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} |
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} |
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return geneIds; |
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} |
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@param |
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@param |
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@throws |
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| 0% |
Uncovered Elements: 5 (5) |
Complexity: 1 |
Complexity Density: 0.2 |
|
290 |
0 |
protected void getTranscripts(AlignmentI al, String accId)... |
291 |
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throws Exception |
292 |
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{ |
293 |
0 |
SequenceI gene = al.getSequenceAt(0); |
294 |
0 |
List<SequenceFeature> transcriptFeatures = getTranscriptFeatures(accId, |
295 |
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gene); |
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297 |
0 |
for (SequenceFeature transcriptFeature : transcriptFeatures) |
298 |
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{ |
299 |
0 |
makeTranscript(transcriptFeature, al, gene); |
300 |
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} |
301 |
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302 |
0 |
clearGeneFeatures(gene); |
303 |
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} |
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@param |
310 |
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| 0% |
Uncovered Elements: 4 (4) |
Complexity: 1 |
Complexity Density: 0.25 |
|
311 |
0 |
protected void clearGeneFeatures(SequenceI gene)... |
312 |
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{ |
313 |
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314 |
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315 |
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316 |
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317 |
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318 |
0 |
String[] soTerms = new String[] { |
319 |
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SequenceOntologyI.NMD_TRANSCRIPT_VARIANT, |
320 |
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SequenceOntologyI.TRANSCRIPT, SequenceOntologyI.EXON, |
321 |
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SequenceOntologyI.CDS }; |
322 |
0 |
List<SequenceFeature> sfs = gene.getFeatures() |
323 |
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.getFeaturesByOntology(soTerms); |
324 |
0 |
for (SequenceFeature sf : sfs) |
325 |
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{ |
326 |
0 |
gene.deleteFeature(sf); |
327 |
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} |
328 |
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} |
329 |
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@param |
337 |
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@param |
338 |
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339 |
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@param |
340 |
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341 |
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@return |
342 |
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| 0% |
Uncovered Elements: 48 (48) |
Complexity: 6 |
Complexity Density: 0.15 |
|
343 |
0 |
SequenceI makeTranscript(SequenceFeature transcriptFeature, AlignmentI al,... |
344 |
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SequenceI gene) |
345 |
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{ |
346 |
0 |
String accId = getTranscriptId(transcriptFeature); |
347 |
0 |
if (accId == null) |
348 |
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{ |
349 |
0 |
return null; |
350 |
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} |
351 |
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352 |
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353 |
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354 |
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355 |
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356 |
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357 |
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358 |
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359 |
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360 |
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361 |
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362 |
0 |
char[] seqChars = new char[gene.getLength()]; |
363 |
0 |
Arrays.fill(seqChars, al.getGapCharacter()); |
364 |
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365 |
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366 |
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367 |
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368 |
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|
369 |
0 |
String parentId = accId; |
370 |
0 |
List<SequenceFeature> splices = findFeatures(gene, |
371 |
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SequenceOntologyI.EXON, parentId); |
372 |
0 |
if (splices.isEmpty()) |
373 |
|
{ |
374 |
0 |
splices = findFeatures(gene, SequenceOntologyI.CDS, parentId); |
375 |
|
} |
376 |
0 |
SequenceFeatures.sortFeatures(splices, true); |
377 |
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|
378 |
0 |
int transcriptLength = 0; |
379 |
0 |
final char[] geneChars = gene.getSequence(); |
380 |
0 |
int offset = gene.getStart(); |
381 |
0 |
List<int[]> mappedFrom = new ArrayList<>(); |
382 |
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|
383 |
0 |
for (SequenceFeature sf : splices) |
384 |
|
{ |
385 |
0 |
int start = sf.getBegin() - offset; |
386 |
0 |
int end = sf.getEnd() - offset; |
387 |
0 |
int spliceLength = end - start + 1; |
388 |
0 |
System.arraycopy(geneChars, start, seqChars, start, spliceLength); |
389 |
0 |
transcriptLength += spliceLength; |
390 |
0 |
mappedFrom.add(new int[] { sf.getBegin(), sf.getEnd() }); |
391 |
|
} |
392 |
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|
393 |
0 |
Sequence transcript = new Sequence(accId, seqChars, 1, |
394 |
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transcriptLength); |
395 |
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396 |
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397 |
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|
398 |
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|
399 |
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|
400 |
0 |
String description = transcriptFeature.getDescription(); |
401 |
0 |
if (description == null) |
402 |
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{ |
403 |
0 |
description = (String) transcriptFeature.getValue(DESCRIPTION); |
404 |
|
} |
405 |
0 |
if (description != null) |
406 |
|
{ |
407 |
0 |
try |
408 |
|
{ |
409 |
0 |
transcript.setDescription(URLDecoder.decode(description, "UTF-8")); |
410 |
|
} catch (UnsupportedEncodingException e) |
411 |
|
{ |
412 |
0 |
e.printStackTrace(); |
413 |
|
} |
414 |
|
} |
415 |
0 |
transcript.createDatasetSequence(); |
416 |
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|
417 |
0 |
al.addSequence(transcript); |
418 |
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419 |
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420 |
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421 |
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422 |
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423 |
0 |
List<int[]> mapTo = new ArrayList<>(); |
424 |
0 |
mapTo.add(new int[] { 1, transcriptLength }); |
425 |
0 |
MapList mapping = new MapList(mappedFrom, mapTo, 1, 1); |
426 |
0 |
EnsemblCdna cdna = new EnsemblCdna(getDomain()); |
427 |
0 |
cdna.transferFeatures(gene.getFeatures().getPositionalFeatures(), |
428 |
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transcript.getDatasetSequence(), mapping, parentId); |
429 |
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|
430 |
0 |
mapTranscriptToChromosome(transcript, gene, mapping); |
431 |
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|
432 |
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433 |
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434 |
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|
435 |
0 |
cdna.getCrossReferences(transcript); |
436 |
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437 |
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438 |
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439 |
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|
440 |
0 |
cdna.addProteinProduct(transcript); |
441 |
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|
442 |
0 |
return transcript; |
443 |
|
} |
444 |
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445 |
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446 |
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447 |
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448 |
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449 |
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@param |
450 |
|
@param |
451 |
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@param |
452 |
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|
453 |
|
|
|
|
| 0% |
Uncovered Elements: 13 (13) |
Complexity: 2 |
Complexity Density: 0.18 |
|
454 |
0 |
protected void mapTranscriptToChromosome(SequenceI transcript,... |
455 |
|
SequenceI gene, MapList mapping) |
456 |
|
{ |
457 |
0 |
GeneLociI loci = gene.getGeneLoci(); |
458 |
0 |
if (loci == null) |
459 |
|
{ |
460 |
0 |
return; |
461 |
|
} |
462 |
|
|
463 |
0 |
MapList geneMapping = loci.getMapping(); |
464 |
|
|
465 |
0 |
List<int[]> exons = mapping.getFromRanges(); |
466 |
0 |
List<int[]> transcriptLoci = new ArrayList<>(); |
467 |
|
|
468 |
0 |
for (int[] exon : exons) |
469 |
|
{ |
470 |
0 |
transcriptLoci.add(geneMapping.locateInTo(exon[0], exon[1])); |
471 |
|
} |
472 |
|
|
473 |
0 |
List<int[]> transcriptRange = Arrays |
474 |
|
.asList(new int[] |
475 |
|
{ transcript.getStart(), transcript.getEnd() }); |
476 |
0 |
MapList mapList = new MapList(transcriptRange, transcriptLoci, 1, 1); |
477 |
|
|
478 |
0 |
transcript.setGeneLoci(loci.getSpeciesId(), loci.getAssemblyId(), |
479 |
|
loci.getChromosomeId(), mapList); |
480 |
|
} |
481 |
|
|
482 |
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|
483 |
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|
484 |
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|
485 |
|
@param |
486 |
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@return |
487 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
488 |
0 |
protected String getTranscriptId(SequenceFeature feature)... |
489 |
|
{ |
490 |
0 |
return (String) feature.getValue(JSON_ID); |
491 |
|
} |
492 |
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493 |
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494 |
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495 |
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496 |
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497 |
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498 |
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499 |
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500 |
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501 |
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502 |
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|
503 |
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@param |
504 |
|
@param |
505 |
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@return |
506 |
|
|
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|
| 100% |
Uncovered Elements: 0 (11) |
Complexity: 2 |
Complexity Density: 0.22 |
|
507 |
1 |
protected List<SequenceFeature> getTranscriptFeatures(String accId,... |
508 |
|
SequenceI geneSequence) |
509 |
|
{ |
510 |
1 |
List<SequenceFeature> transcriptFeatures = new ArrayList<>(); |
511 |
|
|
512 |
1 |
String parentIdentifier = accId; |
513 |
|
|
514 |
1 |
List<SequenceFeature> sfs = geneSequence.getFeatures() |
515 |
|
.getFeaturesByOntology(SequenceOntologyI.TRANSCRIPT); |
516 |
1 |
sfs.addAll(geneSequence.getFeatures().getPositionalFeatures( |
517 |
|
SequenceOntologyI.NMD_TRANSCRIPT_VARIANT)); |
518 |
|
|
519 |
1 |
for (SequenceFeature sf : sfs) |
520 |
|
{ |
521 |
4 |
String parent = (String) sf.getValue(PARENT); |
522 |
4 |
if (parentIdentifier.equalsIgnoreCase(parent)) |
523 |
|
{ |
524 |
3 |
transcriptFeatures.add(sf); |
525 |
|
} |
526 |
|
} |
527 |
|
|
528 |
1 |
return transcriptFeatures; |
529 |
|
} |
530 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
531 |
0 |
@Override... |
532 |
|
public String getDescription() |
533 |
|
{ |
534 |
0 |
return "Fetches all transcripts and variant features for a gene or transcript"; |
535 |
|
} |
536 |
|
|
537 |
|
|
538 |
|
|
539 |
|
|
|
|
| 0% |
Uncovered Elements: 3 (3) |
Complexity: 2 |
Complexity Density: 2 |
|
540 |
0 |
@Override... |
541 |
|
public String getTestQuery() |
542 |
|
{ |
543 |
0 |
return Platform.isJS() ? "ENSG00000123569" : "ENSG00000157764"; |
544 |
|
|
545 |
|
|
546 |
|
|
547 |
|
|
548 |
|
} |
549 |
|
|
550 |
|
|
551 |
|
|
552 |
|
|
553 |
|
|
554 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (9) |
Complexity: 2 |
Complexity Density: 0.29 |
|
555 |
3 |
@Override... |
556 |
|
protected List<SequenceFeature> getIdentifyingFeatures(SequenceI seq, |
557 |
|
String accId) |
558 |
|
{ |
559 |
3 |
List<SequenceFeature> result = new ArrayList<>(); |
560 |
3 |
List<SequenceFeature> sfs = seq.getFeatures() |
561 |
|
.getFeaturesByOntology(SequenceOntologyI.GENE); |
562 |
3 |
for (SequenceFeature sf : sfs) |
563 |
|
{ |
564 |
6 |
String id = (String) sf.getValue(JSON_ID); |
565 |
6 |
if (accId.equalsIgnoreCase(id)) |
566 |
|
{ |
567 |
4 |
result.add(sf); |
568 |
|
} |
569 |
|
} |
570 |
3 |
return result; |
571 |
|
} |
572 |
|
|
573 |
|
|
574 |
|
|
575 |
|
|
576 |
|
|
577 |
|
|
578 |
|
|
579 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (15) |
Complexity: 4 |
Complexity Density: 0.44 |
|
580 |
6 |
@Override... |
581 |
|
protected boolean retainFeature(SequenceFeature sf, String accessionId) |
582 |
|
{ |
583 |
6 |
SequenceOntologyI so = SequenceOntologyFactory.getInstance(); |
584 |
6 |
String type = sf.getType(); |
585 |
6 |
if (so.isA(type, SequenceOntologyI.GENE)) |
586 |
|
{ |
587 |
1 |
return false; |
588 |
|
} |
589 |
5 |
if (isTranscript(type)) |
590 |
|
{ |
591 |
4 |
String parent = (String) sf.getValue(PARENT); |
592 |
4 |
if (!accessionId.equalsIgnoreCase(parent)) |
593 |
|
{ |
594 |
1 |
return false; |
595 |
|
} |
596 |
|
} |
597 |
4 |
return true; |
598 |
|
} |
599 |
|
|
600 |
|
|
601 |
|
|
602 |
|
|
603 |
|
|
|
|
| - |
Uncovered Elements: 0 (0) |
Complexity: 1 |
Complexity Density: - |
|
604 |
0 |
@Override... |
605 |
|
protected void addProteinProduct(SequenceI querySeq) |
606 |
|
{ |
607 |
|
} |
608 |
|
|
|
|
| 0% |
Uncovered Elements: 1 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
609 |
0 |
@Override... |
610 |
|
public Regex getAccessionValidator() |
611 |
|
{ |
612 |
0 |
return ACCESSION_REGEX; |
613 |
|
} |
614 |
|
|
615 |
|
|
616 |
|
|
617 |
|
|
618 |
|
|
619 |
|
|
620 |
|
|
621 |
|
|
622 |
|
|
623 |
|
|
624 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
625 |
3 |
@Override... |
626 |
|
public FeatureSettingsModelI getFeatureColourScheme() |
627 |
|
{ |
628 |
3 |
return new FeatureSettingsAdapter() |
629 |
|
{ |
630 |
|
SequenceOntologyI so = SequenceOntologyFactory.getInstance(); |
631 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
632 |
20 |
@Override... |
633 |
|
public boolean isFeatureHidden(String type) |
634 |
|
{ |
635 |
20 |
return (!so.isA(type, SequenceOntologyI.EXON) |
636 |
|
&& !so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT)); |
637 |
|
} |
638 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (9) |
Complexity: 3 |
Complexity Density: 0.6 |
|
639 |
22 |
@Override... |
640 |
|
public FeatureColourI getFeatureColour(String type) |
641 |
|
{ |
642 |
22 |
if (so.isA(type, SequenceOntologyI.EXON)) |
643 |
|
{ |
644 |
8 |
return new FeatureColour() |
645 |
|
{ |
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
646 |
2 |
@Override... |
647 |
|
public boolean isColourByLabel() |
648 |
|
{ |
649 |
2 |
return true; |
650 |
|
} |
651 |
|
}; |
652 |
|
} |
653 |
14 |
if (so.isA(type, SequenceOntologyI.SEQUENCE_VARIANT)) |
654 |
|
{ |
655 |
12 |
return new FeatureColour() |
656 |
|
{ |
657 |
|
|
|
|
| 100% |
Uncovered Elements: 0 (1) |
Complexity: 1 |
Complexity Density: 1 |
|
658 |
2 |
@Override... |
659 |
|
public Color getColour() |
660 |
|
{ |
661 |
2 |
return Color.RED; |
662 |
|
} |
663 |
|
}; |
664 |
|
} |
665 |
2 |
return null; |
666 |
|
} |
667 |
|
|
668 |
|
|
669 |
|
|
670 |
|
|
|
|
| 64.7% |
Uncovered Elements: 6 (17) |
Complexity: 5 |
Complexity Density: 0.56 |
|
671 |
16 |
@Override... |
672 |
|
public int compare(String feature1, String feature2) |
673 |
|
{ |
674 |
16 |
if (so.isA(feature1, SequenceOntologyI.SEQUENCE_VARIANT)) |
675 |
|
{ |
676 |
12 |
return +1; |
677 |
|
} |
678 |
4 |
if (so.isA(feature2, SequenceOntologyI.SEQUENCE_VARIANT)) |
679 |
|
{ |
680 |
2 |
return -1; |
681 |
|
} |
682 |
2 |
if (so.isA(feature1, SequenceOntologyI.EXON)) |
683 |
|
{ |
684 |
2 |
return +1; |
685 |
|
} |
686 |
0 |
if (so.isA(feature2, SequenceOntologyI.EXON)) |
687 |
|
{ |
688 |
0 |
return -1; |
689 |
|
} |
690 |
0 |
return 0; |
691 |
|
} |
692 |
|
}; |
693 |
|
} |
694 |
|
|
695 |
|
} |