import htsjdk.variant.vcf.VCFHeader;
import htsjdk.variant.vcf.VCFHeaderLine;
+import jalview.analysis.AlignmentUtils;
+import jalview.analysis.Dna;
+import jalview.api.AlignViewControllerGuiI;
import jalview.datamodel.AlignmentI;
-import jalview.datamodel.GeneLoci;
-import jalview.datamodel.Sequence;
+import jalview.datamodel.DBRefEntry;
+import jalview.datamodel.GeneLociI;
+import jalview.datamodel.Mapping;
import jalview.datamodel.SequenceFeature;
import jalview.datamodel.SequenceI;
+import jalview.ext.ensembl.EnsemblMap;
import jalview.ext.htsjdk.VCFReader;
+import jalview.io.gff.Gff3Helper;
import jalview.io.gff.SequenceOntologyI;
import jalview.util.MapList;
+import jalview.util.MappingUtils;
+import jalview.util.MessageManager;
+import java.io.IOException;
+import java.util.HashMap;
import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
+/**
+ * A class to read VCF data (using the htsjdk) and add variants as sequence
+ * features on dna and any related protein product sequences
+ *
+ * @author gmcarstairs
+ */
public class VCFLoader
{
- AlignmentI al;
+ private static final String FEATURE_GROUP_VCF = "VCF";
+
+ private static final String EXCL = "!";
+
+ /*
+ * the alignment we are associated VCF data with
+ */
+ private AlignmentI al;
+
+ /*
+ * mappings between VCF and sequence reference assembly regions, as
+ * key = "species!chromosome!fromAssembly!toAssembly
+ * value = Map{fromRange, toRange}
+ */
+ private Map<String, Map<int[], int[]>> assemblyMappings;
/**
* Constructor given an alignment context
public VCFLoader(AlignmentI alignment)
{
al = alignment;
+
+ // map of species!chromosome!fromAssembly!toAssembly to {fromRange, toRange}
+ assemblyMappings = new HashMap<String, Map<int[], int[]>>();
+ }
+
+ /**
+ * Starts a new thread to query and load VCF variant data on to the alignment
+ * <p>
+ * This method is not thread safe - concurrent threads should use separate
+ * instances of this class.
+ *
+ * @param filePath
+ * @param gui
+ */
+ public void loadVCF(final String filePath,
+ final AlignViewControllerGuiI gui)
+ {
+ if (gui != null)
+ {
+ gui.setStatus(MessageManager.getString("label.searching_vcf"));
+ }
+
+ new Thread()
+ {
+
+ @Override
+ public void run()
+ {
+ VCFLoader.this.doLoad(filePath, gui);
+ }
+
+ }.start();
}
/**
* Loads VCF on to an alignment - provided it can be related to one or more
- * sequence's chromosomal coordinates
+ * sequence's chromosomal coordinates.
*
* @param filePath
+ * @param gui
*/
- public void loadVCF(String filePath)
+ protected void doLoad(String filePath, AlignViewControllerGuiI gui)
{
VCFReader reader = null;
-
try
{
+ // long start = System.currentTimeMillis();
reader = new VCFReader(filePath);
VCFHeader header = reader.getFileHeader();
int varCount = 0;
int seqCount = 0;
+ /*
+ * query for VCF overlapping each sequence in turn
+ */
for (SequenceI seq : al.getSequences())
{
int added = loadVCF(seq, reader, isRefGrch37);
{
seqCount++;
varCount += added;
+ transferAddedFeatures(seq);
}
}
- System.out.println(String.format(
-"Added %d VCF variants to %d sequence(s)", varCount,
- seqCount));
-
- reader.close();
+ if (gui != null)
+ {
+ // long elapsed = System.currentTimeMillis() - start;
+ String msg = MessageManager.formatMessage("label.added_vcf",
+ varCount, seqCount);
+ gui.setStatus(msg);
+ gui.getFeatureSettingsUI().discoverAllFeatureData();
+ }
} catch (Throwable e)
{
System.err.println("Error processing VCF: " + e.getMessage());
e.printStackTrace();
+ if (gui != null)
+ {
+ gui.setStatus("Error occurred - see console for details");
+ }
+ } finally
+ {
+ if (reader != null)
+ {
+ try
+ {
+ reader.close();
+ } catch (IOException e)
+ {
+ // ignore
+ }
+ }
+ }
+ }
+
+ /**
+ * Transfers VCF features to sequences to which this sequence has a mapping.
+ * If the mapping is 1:3, computes peptide variants from nucleotide variants.
+ *
+ * @param seq
+ */
+ protected void transferAddedFeatures(SequenceI seq)
+ {
+ DBRefEntry[] dbrefs = seq.getDBRefs();
+ if (dbrefs == null)
+ {
+ return;
+ }
+ for (DBRefEntry dbref : dbrefs)
+ {
+ Mapping mapping = dbref.getMap();
+ if (mapping == null || mapping.getTo() == null)
+ {
+ continue;
+ }
+
+ SequenceI mapTo = mapping.getTo();
+ MapList map = mapping.getMap();
+ if (map.getFromRatio() == 3)
+ {
+ /*
+ * dna-to-peptide product mapping
+ */
+ AlignmentUtils.computeProteinFeatures(seq, mapTo, map);
+ }
+ else
+ {
+ /*
+ * nucleotide-to-nucleotide mapping e.g. transcript to CDS
+ */
+ // TODO no DBRef to CDS is added to transcripts
+ List<SequenceFeature> features = seq.getFeatures()
+ .getPositionalFeatures(SequenceOntologyI.SEQUENCE_VARIANT);
+ for (SequenceFeature sf : features)
+ {
+ if (FEATURE_GROUP_VCF.equals(sf.getFeatureGroup()))
+ {
+ transferFeature(sf, mapTo, map);
+ }
+ }
+ }
}
}
* @param isVcfRefGrch37
* @return
*/
- protected int loadVCF(SequenceI seq, VCFReader reader, boolean isVcfRefGrch37)
+ protected int loadVCF(SequenceI seq, VCFReader reader,
+ boolean isVcfRefGrch37)
{
int count = 0;
- GeneLoci seqCoords = ((Sequence) seq).getGeneLoci();
+ GeneLociI seqCoords = seq.getGeneLoci();
if (seqCoords == null)
{
return 0;
}
- /*
- * fudge - ensure chromosomal mapping from range is sequence start/end
- * (in case end == 0 when the mapping is first created)
- */
- MapList mapping = seqCoords.getMapping();
- if (mapping.getFromRanges().get(0)[1] == 0)
- {
- mapping.getFromRanges().get(0)[1] = seq.getEnd();
- }
-
- List<int[]> seqChromosomalContigs = mapping.getToRanges();
+ List<int[]> seqChromosomalContigs = seqCoords.getMap().getToRanges();
for (int[] range : seqChromosomalContigs)
{
count += addVcfVariants(seq, reader, range, isVcfRefGrch37);
protected int addVcfVariants(SequenceI seq, VCFReader reader,
int[] range, boolean isVcfRefGrch37)
{
- GeneLoci seqCoords = ((Sequence) seq).getGeneLoci();
+ GeneLociI seqCoords = seq.getGeneLoci();
+
+ String chromosome = seqCoords.getChromosomeId();
+ String seqRef = seqCoords.getAssemblyId();
+ String species = seqCoords.getSpeciesId();
+
+ // TODO handle species properly
+ if ("".equals(species))
+ {
+ species = "human";
+ }
- String chromosome = seqCoords.getChromosome();
- String seqRef = seqCoords.getReference();
- String species = seqCoords.getSpecies();
-
/*
* map chromosomal coordinates from GRCh38 (sequence) to
* GRCh37 (VCF) if necessary
*/
+ // TODO generalise for other assemblies and species
int offset = 0;
- if ("GRCh38".equalsIgnoreCase(seqRef) && isVcfRefGrch37)
+ String fromRef = "GRCh38";
+ if (fromRef.equalsIgnoreCase(seqRef) && isVcfRefGrch37)
{
+ String toRef = "GRCh37";
int[] newRange = mapReferenceRange(range, chromosome, species,
- "GRCh38",
- "GRCh37");
+ fromRef, toRef);
+ if (newRange == null)
+ {
+ System.err.println(String.format(
+ "Failed to map %s:%s:%s:%d:%d to %s", species, chromosome,
+ fromRef, range[0], range[1], toRef));
+ return 0;
+ }
offset = newRange[0] - range[0];
range = newRange;
}
+ boolean forwardStrand = range[0] <= range[1];
+
/*
* query the VCF for overlaps
+ * (convert a reverse strand range to forwards)
*/
int count = 0;
- MapList mapping = seqCoords.getMapping();
+ MapList mapping = seqCoords.getMap();
+ int fromLocus = Math.min(range[0], range[1]);
+ int toLocus = Math.max(range[0], range[1]);
CloseableIterator<VariantContext> variants = reader.query(chromosome,
- range[0], range[1]);
+ fromLocus, toLocus);
while (variants.hasNext())
{
/*
* get variant location in sequence chromosomal coordinates
*/
VariantContext variant = variants.next();
+
+ /*
+ * we can only process SNP variants (which can be reported
+ * as part of a MIXED variant record
+ */
+ if (!variant.isSNP() && !variant.isMixed())
+ {
+ continue;
+ }
+
count++;
int start = variant.getStart() - offset;
int end = variant.getEnd() - offset;
/*
- * get location in sequence coordinates
+ * convert chromosomal location to sequence coordinates
+ * - null if a partially overlapping feature
*/
int[] seqLocation = mapping.locateInFrom(start, end);
- int featureStart = seqLocation[0];
- int featureEnd = seqLocation[1];
- addVariantFeatures(seq, variant, featureStart, featureEnd);
+ if (seqLocation != null)
+ {
+ addVariantFeatures(seq, variant, seqLocation[0], seqLocation[1],
+ forwardStrand);
+ }
}
variants.close();
}
/**
- * Inspects the VCF variant record, and adds variant features to the sequence
+ * Inspects the VCF variant record, and adds variant features to the sequence.
+ * Only SNP variants are added, not INDELs.
+ * <p>
+ * If the sequence maps to the reverse strand of the chromosome, reference and
+ * variant bases are recorded as their complements (C/G, A/T).
*
* @param seq
* @param variant
* @param featureStart
* @param featureEnd
+ * @param forwardStrand
*/
protected void addVariantFeatures(SequenceI seq, VariantContext variant,
- int featureStart, int featureEnd)
+ int featureStart, int featureEnd, boolean forwardStrand)
{
+ byte[] reference = variant.getReference().getBases();
+ if (reference.length != 1)
+ {
+ /*
+ * sorry, we don't handle INDEL variants
+ */
+ return;
+ }
+
+ /*
+ * for now we extract allele frequency as feature score; note
+ * this attribute is String for a simple SNP, but List<String> if
+ * multiple alleles at the locus; we extract for the simple case only
+ */
+ Object af = variant.getAttribute("AF");
+ float score = 0f;
+ if (af instanceof String)
+ {
+ try
+ {
+ score = Float.parseFloat((String) af);
+ } catch (NumberFormatException e)
+ {
+ // leave as 0
+ }
+ }
+
StringBuilder sb = new StringBuilder();
- sb.append(variant.getReference().getBaseString());
+ sb.append(forwardStrand ? (char) reference[0] : complement(reference));
+ /*
+ * inspect alleles and record SNP variants (as the variant
+ * record could be MIXED and include INDEL and SNP alleles)
+ * warning: getAlleles gives no guarantee as to the order
+ * in which they are returned
+ */
for (Allele allele : variant.getAlleles())
{
if (!allele.isReference())
{
- sb.append(",").append(allele.getBaseString());
+ byte[] alleleBase = allele.getBases();
+ if (alleleBase.length == 1)
+ {
+ sb.append(",").append(
+ forwardStrand ? (char) alleleBase[0]
+ : complement(alleleBase));
+ }
}
}
String alleles = sb.toString(); // e.g. G,A,C
String type = SequenceOntologyI.SEQUENCE_VARIANT;
+
SequenceFeature sf = new SequenceFeature(type, alleles, featureStart,
- featureEnd, "VCF");
+ featureEnd, score, FEATURE_GROUP_VCF);
- /*
- * only add 'alleles' property if a SNP, as we can
- * only handle SNPs when computing peptide variants
- */
- if (variant.isSNP())
- {
- sf.setValue("alleles", alleles);
- }
+ sf.setValue(Gff3Helper.ALLELES, alleles);
Map<String, Object> atts = variant.getAttributes();
for (Entry<String, Object> att : atts.entrySet())
}
/**
- * Call the Ensembl REST service that maps from one assembly reference's
- * coordinates to another's
+ * A convenience method to complement a dna base and return the string value
+ * of its complement
*
- * @param range
+ * @param reference
+ * @return
+ */
+ protected String complement(byte[] reference)
+ {
+ return String.valueOf(Dna.getComplement((char) reference[0]));
+ }
+
+ /**
+ * Determines the location of the query range (chromosome positions) in a
+ * different reference assembly.
+ * <p>
+ * If the range is just a subregion of one for which we already have a mapping
+ * (for example, an exon sub-region of a gene), then the mapping is just
+ * computed arithmetically.
+ * <p>
+ * Otherwise, calls the Ensembl REST service that maps from one assembly
+ * reference's coordinates to another's
+ *
+ * @param queryRange
+ * start-end chromosomal range in 'fromRef' coordinates
+ * @param chromosome
+ * @param species
+ * @param fromRef
+ * assembly reference for the query coordinates
+ * @param toRef
+ * assembly reference we wish to translate to
+ * @return the start-end range in 'toRef' coordinates
+ */
+ protected int[] mapReferenceRange(int[] queryRange, String chromosome,
+ String species, String fromRef, String toRef)
+ {
+ /*
+ * first try shorcut of computing the mapping as a subregion of one
+ * we already have (e.g. for an exon, if we have the gene mapping)
+ */
+ int[] mappedRange = findSubsumedRangeMapping(queryRange, chromosome,
+ species, fromRef, toRef);
+ if (mappedRange != null)
+ {
+ return mappedRange;
+ }
+
+ /*
+ * call (e.g.) http://rest.ensembl.org/map/human/GRCh38/17:45051610..45109016:1/GRCh37
+ */
+ EnsemblMap mapper = new EnsemblMap();
+ int[] mapping = mapper.getMapping(species, chromosome, fromRef, toRef,
+ queryRange);
+
+ if (mapping == null)
+ {
+ // mapping service failure
+ return null;
+ }
+
+ /*
+ * save mapping for possible future re-use
+ */
+ String key = makeRangesKey(chromosome, species, fromRef, toRef);
+ if (!assemblyMappings.containsKey(key))
+ {
+ assemblyMappings.put(key, new HashMap<int[], int[]>());
+ }
+
+ assemblyMappings.get(key).put(queryRange, mapping);
+
+ return mapping;
+ }
+
+ /**
+ * If we already have a 1:1 contiguous mapping which subsumes the given query
+ * range, this method just calculates and returns the subset of that mapping,
+ * else it returns null. In practical terms, if a gene has a contiguous
+ * mapping between (for example) GRCh37 and GRCh38, then we assume that its
+ * subsidiary exons occupy unchanged relative positions, and just compute
+ * these as offsets, rather than do another lookup of the mapping.
+ * <p>
+ * If in future these assumptions prove invalid (e.g. for bacterial dna?!),
+ * simply remove this method or let it always return null.
+ * <p>
+ * Warning: many rapid calls to the /map service map result in a 429 overload
+ * error response
+ *
+ * @param queryRange
* @param chromosome
* @param species
* @param fromRef
* @param toRef
* @return
*/
- protected int[] mapReferenceRange(int[] range, String chromosome,
+ protected int[] findSubsumedRangeMapping(int[] queryRange, String chromosome,
String species, String fromRef, String toRef)
{
- // TODO call
- // http://rest.ensembl.org/map/species/fromRef/chromosome:range[0]..range[1]:1/toRef?content-type=application/json
- // and parse the JSON response
+ String key = makeRangesKey(chromosome, species, fromRef, toRef);
+ if (assemblyMappings.containsKey(key))
+ {
+ Map<int[], int[]> mappedRanges = assemblyMappings.get(key);
+ for (Entry<int[], int[]> mappedRange : mappedRanges.entrySet())
+ {
+ int[] fromRange = mappedRange.getKey();
+ int[] toRange = mappedRange.getValue();
+ if (fromRange[1] - fromRange[0] == toRange[1] - toRange[0])
+ {
+ /*
+ * mapping is 1:1 in length, so we trust it to have no discontinuities
+ */
+ if (MappingUtils.rangeContains(fromRange, queryRange))
+ {
+ /*
+ * fromRange subsumes our query range
+ */
+ int offset = queryRange[0] - fromRange[0];
+ int mappedRangeFrom = toRange[0] + offset;
+ int mappedRangeTo = mappedRangeFrom + (queryRange[1] - queryRange[0]);
+ return new int[] { mappedRangeFrom, mappedRangeTo };
+ }
+ }
+ }
+ }
+ return null;
+ }
+
+ /**
+ * 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 mapping
+ * mapping from the feature's coordinates to the target sequence
+ */
+ protected void transferFeature(SequenceFeature sf,
+ SequenceI targetSequence, MapList mapping)
+ {
+ int[] mappedRange = mapping.locateInTo(sf.getBegin(), sf.getEnd());
+
+ if (mappedRange != null)
+ {
+ String group = sf.getFeatureGroup();
+ int newBegin = Math.min(mappedRange[0], mappedRange[1]);
+ int newEnd = Math.max(mappedRange[0], mappedRange[1]);
+ SequenceFeature copy = new SequenceFeature(sf, newBegin, newEnd,
+ group, sf.getScore());
+ targetSequence.addSequenceFeature(copy);
+ }
+ }
- // 1922632 is the difference between 37 and 38 for chromosome 17
- return new int[] { range[0] - 1922632, range[1] - 1922632 };
+ /**
+ * Formats a ranges map lookup key
+ *
+ * @param chromosome
+ * @param species
+ * @param fromRef
+ * @param toRef
+ * @return
+ */
+ protected static String makeRangesKey(String chromosome, String species,
+ String fromRef, String toRef)
+ {
+ return species + EXCL + chromosome + EXCL + fromRef + EXCL
+ + toRef;
}
}
git://source.jalview.org / jalview.git / blobdiff