package jalview.ext.ensembl;
-import jalview.datamodel.AlignedCodonFrame;
import jalview.datamodel.AlignmentI;
+import jalview.datamodel.Sequence;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
import jalview.io.gff.SequenceOntology;
import jalview.util.MapList;
import java.util.ArrayList;
+import java.util.Arrays;
import java.util.List;
/**
@Override
public AlignmentI getSequenceRecords(String query) throws Exception
{
+ // TODO ? if an ENST identifier is supplied, convert to ENSG?
AlignmentI al = super.getSequenceRecords(query);
if (al.getHeight() > 0)
{
}
/**
- * Find and fetch all transcripts for the gene, as identified by "transcript"
- * features whose Parent is the requested gene
+ * Constructs all transcripts for the gene, as identified by "transcript"
+ * features whose Parent is the requested gene. The coding transcript
+ * sequences (i.e. with introns omitted) are added to the alignment.
*
* @param al
* @param accId
throws Exception
{
SequenceI gene = al.getSequenceAt(0);
- List<String> transcriptIds = getTranscriptIds(accId, gene);
+ List<SequenceFeature> transcriptFeatures = getTranscriptFeatures(accId,
+ gene);
- // TODO: could just use features and genomic sequence
- // to generate the transcript sequences - faster
- // could also grab "Name" as transcript description (gene name)
- for (String transcriptId : transcriptIds)
+ for (SequenceFeature transcriptFeature : transcriptFeatures)
{
- /*
- * fetch and map the transcript sequence; we can pass in the gene
- * sequence with features marked to save fetching it again
- */
- EnsemblCdna cdnaFetcher = new EnsemblCdna();
- AlignmentI al2 = cdnaFetcher.getSequenceRecords(transcriptId,
- gene);
- for (SequenceI seq : al2.getSequences())
- {
- /*
- * build mapping from gene sequence to transcript
- */
- MapList mapping = cdnaFetcher.getGenomicRanges(gene, transcriptId,
- seq.getStart());
-
- /*
- * align the transcript to the gene
- */
- AlignedCodonFrame acf = new AlignedCodonFrame();
- acf.addMap(gene, seq, mapping);
- char gap = al.getGapCharacter();
- // AlignmentUtils.alignSequenceAs(seq, gene, acf, String.valueOf(gap),
- // gap, false, false);
-
- al.addSequence(seq);
- }
+ makeTranscript(transcriptFeature, al, gene);
}
}
/**
- * Returns a list of the ids of transcript features on the sequence whose
- * Parent is the gene for the accession id
+ * Constructs a spliced transcript sequence by finding 'exon' features for the
+ * given id (or failing that 'CDS'). Copies features on to the new sequence.
+ * 'Aligns' the new sequence against the gene sequence by padding with gaps,
+ * and adds it to the alignment.
*
- * @param accId
- * @param geneSequence
+ * @param transcriptFeature
+ * @param al
+ * the alignment to which to add the new sequence
+ * @param gene
+ * the parent gene sequence, with features
* @return
*/
- protected List<String> getTranscriptIds(String accId, SequenceI geneSequence)
+ SequenceI makeTranscript(SequenceFeature transcriptFeature,
+ AlignmentI al, SequenceI gene)
{
- SequenceOntology so = SequenceOntology.getInstance();
- List<String> transcriptIds = new ArrayList<String>();
+ String accId = (String) transcriptFeature.getValue("transcript_id");
+ if (accId == null)
+ {
+ return null;
+ }
/*
- * scan for transcript features belonging to our gene;
- * also remove any which belong to other genes
+ * NB we are mapping from gene sequence (not genome), so do not
+ * need to check for reverse strand (gene and transcript sequences
+ * are in forward sense)
*/
- SequenceFeature[] sfs = geneSequence.getSequenceFeatures();
+
+ /*
+ * make a gene-length sequence filled with gaps
+ * we will fill in the bases for transcript regions
+ */
+ char[] seqChars = new char[gene.getLength()];
+ Arrays.fill(seqChars, al.getGapCharacter());
+
+ /*
+ * look for exon features of the transcript, failing that for CDS
+ * (for example ENSG00000124610 has 1 CDS but no exon features)
+ */
+ String parentId = "transcript:" + accId;
+ List<SequenceFeature> splices = findFeatures(gene,
+ SequenceOntology.EXON, parentId);
+ if (splices.isEmpty())
+ {
+ splices = findFeatures(gene, SequenceOntology.CDS, parentId);
+ }
+
+ int transcriptLength = 0;
+ final char[] geneChars = gene.getSequence();
+ int offset = gene.getStart(); // to convert to 0-based positions
+ List<int[]> mappedFrom = new ArrayList<int[]>();
+
+ for (SequenceFeature sf : splices)
+ {
+ int start = sf.getBegin() - offset;
+ int end = sf.getEnd() - offset;
+ int spliceLength = end - start + 1;
+ System.arraycopy(geneChars, start, seqChars, start, spliceLength);
+ transcriptLength += spliceLength;
+ mappedFrom.add(new int[] { sf.getBegin(), sf.getEnd() });
+ }
+
+ Sequence transcript = new Sequence(accId, seqChars, 1, transcriptLength);
+ transcript.createDatasetSequence();
+
+ al.addSequence(transcript);
+
+ /*
+ * transfer features to the new sequence; we use EnsemblCdna to do this,
+ * to filter out unwanted features types (see method retainFeature)
+ */
+ List<int[]> mapTo = new ArrayList<int[]>();
+ mapTo.add(new int[] { 1, transcriptLength });
+ MapList mapping = new MapList(mappedFrom, mapTo, 1, 1);
+ new EnsemblCdna().transferFeatures(gene.getSequenceFeatures(),
+ transcript.getDatasetSequence(), mapping, parentId);
+
+ /*
+ * and finally fetch the protein product and save as a cross-reference
+ */
+ addProteinProduct(transcript);
+
+ return transcript;
+ }
+
+ /**
+ * Returns a list of the transcript features on the sequence whose Parent is
+ * the gene for the accession id. Also removes all transcript features from
+ * the gene sequence, as we have no further need for them and they obscure
+ * more useful features on the display.
+ *
+ * @param accId
+ * @param geneSequence
+ * @return
+ */
+ protected List<SequenceFeature> getTranscriptFeatures(String accId,
+ SequenceI geneSequence)
+ {
+ List<SequenceFeature> transcriptFeatures = new ArrayList<SequenceFeature>();
+
List<SequenceFeature> keptFeatures = new ArrayList<SequenceFeature>();
- boolean featureDropped = false;
String parentIdentifier = "gene:" + accId;
- for (SequenceFeature sf : sfs)
+ SequenceFeature[] sfs = geneSequence.getSequenceFeatures();
+
+ if (sfs != null)
{
- if (so.isA(sf.getType(), SequenceOntology.TRANSCRIPT))
+ for (SequenceFeature sf : sfs)
{
- String parent = (String) sf.getValue(PARENT);
- if (parentIdentifier.equals(parent))
+ if (isTranscript(sf.getType()))
{
- transcriptIds.add((String) sf.getValue("transcript_id"));
- keptFeatures.add(sf);
+ String parent = (String) sf.getValue(PARENT);
+ if (parentIdentifier.equals(parent))
+ {
+ transcriptFeatures.add(sf);
+ }
}
else
{
- featureDropped = true;
+ keptFeatures.add(sf);
}
}
- else
- {
- keptFeatures.add(sf);
- }
- }
- if (featureDropped)
- {
- geneSequence.getDatasetSequence().setSequenceFeatures(
- keptFeatures.toArray(new SequenceFeature[keptFeatures
- .size()]));
}
- return transcriptIds;
+ SequenceFeature[] featuresRetained = keptFeatures.toArray(new SequenceFeature[keptFeatures.size()]);
+ geneSequence.getDatasetSequence().setSequenceFeatures(featuresRetained);
+
+ return transcriptFeatures;
}
@Override
@Override
public String getTestQuery()
{
- return "ENSG00000157764"; // reverse strand
- // ENSG00000090266 // forward strand
+ return "ENSG00000157764"; // BRAF, 5 transcripts, reverse strand
+ // ENSG00000090266 // NDUFB2, 15 transcripts, forward strand
+ // ENSG00000101812 // H2BFM histone, 3 transcripts, forward strand
+ // ENSG00000123569 // H2BFWT histone, 2 transcripts, reverse strand
}
/**
}
/**
- * 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);
+ if (SequenceOntology.getInstance().isA(sf.getType(),
+ SequenceOntology.GENE))
+ {
+ return false;
+ }
+
+ if (isTranscript(sf.getType()))
+ {
+ String parent = (String) sf.getValue(PARENT);
+ if (!("gene:" + accessionId).equals(parent))
+ {
+ return false;
+ }
+ }
+ return true;
+ }
+
+ /**
+ * Answers false. This allows an optimisation - a single 'gene' feature is all
+ * that is needed to identify the positions of the gene on the genomic
+ * sequence.
+ */
+ @Override
+ protected boolean isSpliceable()
+ {
+ return false;
}
}
git://source.jalview.org / jalview.git / blobdiff