*/
public abstract class EnsemblSeqProxy extends EnsemblRestClient
{
+ protected static final String CONSEQUENCE_TYPE = "consequence_type";
+
protected static final String PARENT = "Parent";
protected static final String ID = "ID";
+ /*
+ * this needs special handling, as it isA sequence_variant in the
+ * Sequence Ontology, but behaves in Ensembl as if it isA transcript
+ */
+ protected static final String NMD_VARIANT = "NMD_transcript_variant";
+
public enum EnsemblSeqType
{
/**
}
- /*
- * genomic sequence, with features retrieved from the REST overlap service
- */
- private SequenceI genomicSequence;
-
/**
* Constructor
*/
/**
* Makes the sequence queries to Ensembl's REST service and returns an
- * alignment consisting of the returned sequences
+ * alignment consisting of the returned sequences. This overloaded method
+ * allows the genomic sequence (with features) to be passed in if it has
+ * already been retrieved, to avoid repeat calls to fetch it.
*/
- @Override
- public AlignmentI getSequenceRecords(String query) throws Exception
+ public AlignmentI getSequenceRecords(String query,
+ SequenceI genomicSequence) throws Exception
{
long now = System.currentTimeMillis();
// TODO use a String... query vararg instead?
// danger: accession separator used as a regex here, a string elsewhere
// in this case it is ok (it is just a space), but (e.g.) '\' would not be
- List<String> allIds = Arrays.asList(query.split(getAccessionSeparator()));
+ List<String> allIds = Arrays.asList(query
+ .split(getAccessionSeparator()));
AlignmentI alignment = null;
inProgress = true;
*/
for (String accId : allIds)
{
- addFeaturesAndProduct(accId, alignment);
+ addFeaturesAndProduct(accId, alignment, genomicSequence);
}
inProgress = false;
* @param accId
* @param alignment
*/
- protected void addFeaturesAndProduct(String accId, AlignmentI alignment)
+ protected void addFeaturesAndProduct(String accId, AlignmentI alignment,
+ SequenceI genomicSequence)
{
try
{
features);
if (geneFeatures.getHeight() > 0)
{
- /*
- * transfer features to the query sequence
- */
genomicSequence = geneFeatures.getSequenceAt(0);
}
}
if (genomicSequence != null)
{
+ /*
+ * transfer features to the query sequence
+ */
SequenceI querySeq = alignment.findName(accId);
if (transferFeatures(accId, genomicSequence, querySeq))
{
* dna here since the retrieved sequence is as transcribed (reverse
* complement for reverse strand), i.e in the same sense as the peptide.
*/
+ boolean fivePrimeIncomplete = false;
for (SequenceFeature sf : sfs)
{
/*
*/
if (so.isA(sf.getType(), SequenceOntology.CDS))
{
- ranges.add(new int[] { sf.getBegin(), sf.getEnd() });
- mappedDnaLength += Math.abs(sf.getEnd() - sf.getBegin()) + 1;
+ int phase = 0;
+ try {
+ phase = Integer.parseInt(sf.getPhase());
+ } catch (NumberFormatException e)
+ {
+ // ignore
+ }
+ /*
+ * phase > 0 on first codon means 5' incomplete - skip to the start
+ * of the next codon; example ENST00000496384
+ */
+ int begin = sf.getBegin();
+ int end = sf.getEnd();
+ if (ranges.isEmpty() && phase > 0)
+ {
+ fivePrimeIncomplete = true;
+ begin += phase;
+ if (begin > end)
+ {
+ continue; // shouldn't happen?
+ }
+ }
+ ranges.add(new int[] { begin, end });
+ mappedDnaLength += Math.abs(end - begin) + 1;
}
}
int proteinLength = proteinSeq.getLength();
List<int[]> proteinRange = new ArrayList<int[]>();
- proteinRange.add(new int[] { 1, proteinLength });
+ int proteinStart = 1;
+ if (fivePrimeIncomplete && proteinSeq.getCharAt(0) == 'X')
+ {
+ proteinStart = 2;
+ proteinLength--;
+ }
+ proteinRange.add(new int[] { proteinStart, proteinLength });
/*
- * dna length should map to protein (or protein minus stop codon)
+ * dna length should map to protein (or protein plus stop codon)
*/
- if (mappedDnaLength == 3 * proteinLength
- || mappedDnaLength == 3 * (proteinLength + 1))
+ int codesForResidues = mappedDnaLength / 3;
+ if (codesForResidues == proteinLength
+ || codesForResidues == (proteinLength + 1))
{
return new MapList(ranges, proteinRange, 3, 1);
}
}
/*
- * generously size for initial number of cds regions
+ * generously initial size for number of cds regions
* (worst case titin Q8WZ42 has c. 313 exons)
*/
List<int[]> regions = new ArrayList<int[]>(100);
- int sourceLength = sourceSequence.getLength();
int mappedLength = 0;
int direction = 1; // forward
boolean directionSet = false;
}
mappedLength += Math.abs(sf.getEnd() - sf.getBegin() + 1);
- if (mappedLength >= sourceLength)
+ if (!isSpliceable())
{
/*
- * break for the case of matching gene features v gene sequence
- * - only need to locate the 'gene' feature for accId
+ * 'gene' sequence is contiguous so we can stop as soon as its
+ * identifying feature has been found
*/
break;
}
}
/**
+ * Answers true if the sequence being retrieved may occupy discontiguous
+ * regions on the genomic sequence.
+ */
+ protected boolean isSpliceable()
+ {
+ return true;
+ }
+
+ /**
* Returns true if the sequence feature marks positions of the genomic
* sequence feature which are within the sequence being retrieved. For
* example, an 'exon' feature whose parent is the target transcript marks the
String accId);
/**
- * Transfers the sequence feature to the target sequence, adjusting its start
- * and end range based on the 'overlap' ranges. Features which do not overlap
- * the target sequence are ignored, as are features with a parent other than
- * the target sequence id.
+ * Transfers the sequence feature to the target sequence, locating its start
+ * and end range based on the mapping. Features which do not overlap the
+ * target sequence are ignored.
*
* @param sf
* @param targetSequence
- * @param overlap
+ * @param mapping
+ * mapping from the sequence feature's coordinates to the target
+ * sequence
*/
protected void transferFeature(SequenceFeature sf,
- SequenceI targetSequence, MapList overlap)
+ SequenceI targetSequence, MapList mapping)
{
int start = sf.getBegin();
int end = sf.getEnd();
- int[] mappedRange = overlap.locateInTo(start, end);
+ int[] mappedRange = mapping.locateInTo(start, end);
if (mappedRange != null)
{
*/
if (SequenceOntology.getInstance().isSequenceVariant(sf.getType()))
{
- String consequence = (String) sf.getValue("consequence_type");
+ String consequence = (String) sf.getValue(CONSEQUENCE_TYPE);
if (consequence != null)
{
SequenceFeature sf2 = new SequenceFeature("consequence",
}
}
}
-
}
/**
}
SequenceFeature[] sfs = sourceSequence.getSequenceFeatures();
- MapList overlap = getGenomicRanges(sourceSequence, accessionId,
+ MapList mapping = getGenomicRanges(sourceSequence, accessionId,
targetSequence.getStart());
- if (overlap == null)
+ if (mapping == null)
{
return false;
}
- final boolean forwardStrand = overlap.isFromForwardStrand();
+ return transferFeatures(sfs, targetSequence, mapping, accessionId);
+ }
+
+ /**
+ * Transfer features to the target sequence. The start/end positions are
+ * converted using the mapping. Features which do not overlap are ignored.
+ * Features whose parent is not the specified identifier are also ignored.
+ *
+ * @param features
+ * @param targetSequence
+ * @param mapping
+ * @param parentId
+ * @return
+ */
+ protected boolean transferFeatures(SequenceFeature[] features,
+ SequenceI targetSequence, MapList mapping, String parentId)
+ {
+ final boolean forwardStrand = mapping.isFromForwardStrand();
/*
* sort features by start position (descending if reverse strand)
* before transferring (in forwards order) to the target sequence
*/
- Arrays.sort(sfs, new Comparator<SequenceFeature>()
+ Arrays.sort(features, new Comparator<SequenceFeature>()
{
@Override
public int compare(SequenceFeature o1, SequenceFeature o2)
});
boolean transferred = false;
- for (SequenceFeature sf : sfs)
+ for (SequenceFeature sf : features)
{
- if (retainFeature(sf, accessionId))
+ if (retainFeature(sf, parentId))
{
- transferFeature(sf, targetSequence, overlap);
+ transferFeature(sf, targetSequence, mapping);
transferred = true;
}
}
}
/**
- * Answers true if the feature is one to attach to the retrieved sequence
+ * Answers true if the feature type is one we want to keep for the sequence.
+ * Some features are only retrieved in order to identify the sequence range,
+ * and may then be discarded as redundant information (e.g. "CDS" feature for
+ * a CDS sequence).
+ */
+ @SuppressWarnings("unused")
+ protected boolean retainFeature(SequenceFeature sf, String accessionId)
+ {
+ return true; // override as required
+ }
+
+ /**
+ * Answers true if the feature has a Parent which refers to the given
+ * accession id, or if the feature has no parent. Answers false if the
+ * feature's Parent is for a different accession id.
*
- * @param type
+ * @param sf
+ * @param identifier
* @return
*/
- protected boolean retainFeature(SequenceFeature sf, String accessionId)
+ protected boolean featureMayBelong(SequenceFeature sf, String identifier)
{
String parent = (String) sf.getValue(PARENT);
- if (parent != null && !parent.contains(accessionId))
+ // using contains to allow for prefix "gene:", "transcript:" etc
+ if (parent != null && !parent.contains(identifier))
{
// this genomic feature belongs to a different transcript
return false;
+ " sequence with variant features";
}
- public AlignmentI getSequenceRecords(String transcriptId,
- SequenceI geneSeq) throws Exception
+ @Override
+ public AlignmentI getSequenceRecords(String identifier) throws Exception
+ {
+ return getSequenceRecords(identifier, null);
+ }
+
+ /**
+ * Returns a (possibly empty) list of features on the sequence which have the
+ * specified sequence ontology type (or a sub-type of it), and the given
+ * identifier as parent
+ *
+ * @param sequence
+ * @param type
+ * @param parentId
+ * @return
+ */
+ protected List<SequenceFeature> findFeatures(SequenceI sequence,
+ String type, String parentId)
+ {
+ List<SequenceFeature> result = new ArrayList<SequenceFeature>();
+
+ SequenceFeature[] sfs = sequence.getSequenceFeatures();
+ if (sfs != null) {
+ SequenceOntology so = SequenceOntology.getInstance();
+ for (SequenceFeature sf :sfs) {
+ if (so.isA(sf.getType(), type))
+ {
+ String parent = (String) sf.getValue(PARENT);
+ if (parent.equals(parentId))
+ {
+ result.add(sf);
+ }
+ }
+ }
+ }
+ return result;
+ }
+
+ /**
+ * Answers true if the feature type is either 'NMD_transcript_variant' or
+ * 'transcript' or one of its sub-types in the Sequence Ontology. This is
+ * needed because NMD_transcript_variant behaves like 'transcript' in Ensembl
+ * although strictly speaking it is not (it is a sub-type of
+ * sequence_variant).
+ *
+ * @param featureType
+ * @return
+ */
+ public static boolean isTranscript(String featureType)
{
- this.genomicSequence = geneSeq;
- return getSequenceRecords(transcriptId);
+ return NMD_VARIANT.equals(featureType)
+ || SequenceOntology.getInstance().isA(featureType, SequenceOntology.TRANSCRIPT);
}
}
git://source.jalview.org / jalview.git / blobdiff