* keys to fields of VEP CSQ consequence data
* see https://www.ensembl.org/info/docs/tools/vep/vep_formats.html
*/
- private static final String ALLELE_NUM_KEY = "ALLELE_NUM"; // 0 (ref), 1...
+ private static final String ALLELE_KEY = "Allele";
+ private static final String ALLELE_NUM_KEY = "ALLELE_NUM"; // 0 (ref), 1...
private static final String FEATURE_KEY = "Feature"; // Ensembl stable id
/*
+ * what comes before column headings in CSQ Description field
+ */
+ private static final String FORMAT = "Format: ";
+
+ /*
* default VCF INFO key for VEP consequence data
* NB this can be overridden running VEP with --vcf_info_field
* - we don't handle this case (require CSQ identifier)
private static final String COMMA = ",";
/*
- * (temporary) flag that determines whether Jalview adds one feature
- * per VCF record, or one per allele (preferred)
- */
- private static final boolean FEATURE_PER_ALLELE = true;
-
- /*
* the feature group assigned to a VCF variant in Jalview
*/
private static final String FEATURE_GROUP_VCF = "VCF";
private VCFHeader header;
/*
- * the position (0...) of the ALLELE_NUM field in each block of
+ * the position (0...) of field in each block of
* CSQ (consequence) data (if declared in the VCF INFO header for CSQ)
* see http://www.ensembl.org/info/docs/tools/vep/vep_formats.html
*/
+ private int csqAlleleFieldIndex = -1;
private int csqAlleleNumberFieldIndex = -1;
-
private int csqFeatureFieldIndex = -1;
/**
.getOtherHeaderLine(VCFHeader.REFERENCE_KEY);
/*
- * note offset of CSQ ALLELE_NUM field if it is declared
+ * get offset of CSQ ALLELE_NUM and Feature if declared
*/
locateCsqFields();
*/
for (SequenceI seq : al.getSequences())
{
- int added = loadVCF(seq, reader, isRefGrch37);
+ int added = loadSequenceVCF(seq, reader, isRefGrch37);
if (added > 0)
{
seqCount++;
}
/**
- * Records the position of fields for ALLELE_NUM and Feature defined in the
- * CSQ INFO header (if there is one). CSQ fields are declared in the CSQ INFO
- * Description e.g.
+ * Records the position of selected fields defined in the CSQ INFO header (if
+ * there is one). CSQ fields are declared in the CSQ INFO Description e.g.
* <p>
* Description="Consequence ...from ... VEP. Format: Allele|Consequence|...
*/
}
String desc = csqInfo.getDescription();
+ int formatPos = desc.indexOf(FORMAT);
+ if (formatPos == -1)
+ {
+ System.err.println("Parse error, failed to find " + FORMAT
+ + " in " + desc);
+ return;
+ }
+ desc = desc.substring(formatPos + FORMAT.length());
+
if (desc != null)
{
String[] format = desc.split(PIPE_REGEX);
{
csqAlleleNumberFieldIndex = index;
}
+ if (ALLELE_KEY.equals(field))
+ {
+ csqAlleleFieldIndex = index;
+ }
if (FEATURE_KEY.equals(field))
{
csqFeatureFieldIndex = index;
* @param isVcfRefGrch37
* @return
*/
- protected int loadVCF(SequenceI seq, VCFReader reader,
+ protected int loadSequenceVCF(SequenceI seq, VCFReader reader,
boolean isVcfRefGrch37)
{
int count = 0;
*/
if (!variant.isSNP() && !variant.isMixed())
{
- continue;
+ // continue;
}
int start = variant.getStart() - offset;
int[] seqLocation = mapping.locateInFrom(start, end);
if (seqLocation != null)
{
- count += addVariantFeature(seq, variant, seqLocation[0],
+ count += addAlleleFeatures(seq, variant, seqLocation[0],
seqLocation[1], forwardStrand);
}
}
}
/**
- * Inspects the VCF variant record, and adds variant features to the sequence.
- * Only SNP variants are added, not INDELs. Returns the number of features
- * added.
- * <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 int addVariantFeature(SequenceI seq, VariantContext variant,
- int featureStart, int featureEnd, boolean forwardStrand)
- {
- byte[] reference = variant.getReference().getBases();
- if (reference.length != 1)
- {
- /*
- * sorry, we don't handle INDEL variants
- */
- return 0;
- }
-
- if (FEATURE_PER_ALLELE)
- {
- return addAlleleFeatures(seq, variant, featureStart, featureEnd,
- forwardStrand);
- }
-
- /*
- * 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
- */
- float score = getAlleleFrequency(variant, 0);
-
- StringBuilder sb = new StringBuilder();
- 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())
- {
- byte[] alleleBase = allele.getBases();
- if (alleleBase.length == 1)
- {
- sb.append(COMMA).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, score, FEATURE_GROUP_VCF);
-
- sf.setValue(Gff3Helper.ALLELES, alleles);
-
- Map<String, Object> atts = variant.getAttributes();
- for (Entry<String, Object> att : atts.entrySet())
- {
- sf.setValue(att.getKey(), att.getValue());
- }
- seq.addSequenceFeature(sf);
-
- return 1;
- }
-
- /**
* A convenience method to get the AF value for the given alternate allele
* index
*
}
/**
- * Adds one variant feature for each SNP allele in the VCF variant record, and
+ * Adds one variant feature for each allele in the VCF variant record, and
* returns the number of features added.
*
* @param seq
/**
* Inspects one allele and attempts to add a variant feature for it to the
- * sequence. Only SNP variants are added as features. We extract as much as
- * possible of the additional data associated with this allele to store in the
- * feature's key-value map. Answers the number of features added (0 or 1).
+ * sequence. We extract as much as possible of the additional data associated
+ * with this allele to store in the feature's key-value map. Answers the
+ * number of features added (0 or 1).
*
* @param seq
* @param variant
* @param altAlleleIndex
+ * (0, 1..)
* @param featureStart
* @param featureEnd
* @param forwardStrand
int altAlleleIndex, int featureStart, int featureEnd,
boolean forwardStrand)
{
- byte[] reference = variant.getReference().getBases();
+ String reference = variant.getReference().getBaseString();
Allele alt = variant.getAlternateAllele(altAlleleIndex);
- byte[] allele = alt.getBases();
- if (allele.length != 1)
+ String allele = alt.getBaseString();
+ if (allele.length() != 1)
{
/*
* not a SNP variant
*/
- return 0;
+ // return 0;
}
/*
- * build the ref,alt allele description e.g. "G,A"
+ * build the ref,alt allele description e.g. "G,A", using the base
+ * complement if the sequence is on the reverse strand
*/
+ // TODO check how structural variants are shown on reverse strand
StringBuilder sb = new StringBuilder();
- sb.append(forwardStrand ? (char) reference[0] : complement(reference));
+ sb.append(forwardStrand ? reference : Dna.reverseComplement(reference));
sb.append(COMMA);
- sb.append(forwardStrand ? (char) allele[0] : complement(allele));
+ sb.append(forwardStrand ? allele : Dna.reverseComplement(allele));
String alleles = sb.toString(); // e.g. G,A
String type = SequenceOntologyI.SEQUENCE_VARIANT;
* @param seq
* @param sf
* @param altAlelleIndex
+ * (0, 1..)
*/
protected void addAlleleProperties(VariantContext variant, SequenceI seq,
SequenceFeature sf, final int altAlelleIndex)
* extract Consequence data (if present) that we are able to
* associated with the allele for this variant feature
*/
- if (CSQ.equals(key) && csqAlleleNumberFieldIndex > -1)
+ if (CSQ.equals(key))
{
- addConsequences(att.getValue(), seq, sf, altAlelleIndex + 1);
+ addConsequences(variant, seq, sf, altAlelleIndex);
return;
}
* Inspects CSQ data blocks (consequences) and adds attributes on the sequence
* feature for the current allele (and transcript if applicable)
* <p>
- * Allele matching: we require field ALLELE_NUM to match altAlleleIndex. If
- * the CSQ data does not include ALLELE_NUM values then no data is added to
- * the variant feature.
+ * Allele matching: if field ALLELE_NUM is present, it must match
+ * altAlleleIndex. If not present, then field Allele value must match the VCF
+ * Allele.
* <p>
* Transcript matching: if sequence name can be identified to at least one of
* the consequences' Feature values, then select only consequences that match
* take all consequences (this is the case when adding features to the gene
* sequence).
*
- * @param value
+ * @param variant
* @param seq
* @param sf
* @param altAlelleIndex
- * (1=first alternative allele...)
+ * (0, 1..)
*/
- protected void addConsequences(Object value, SequenceI seq,
+ protected void addConsequences(VariantContext variant, SequenceI seq,
SequenceFeature sf, int altAlelleIndex)
{
- if (!(value instanceof ArrayList<?>))
+ Object value = variant.getAttribute(CSQ);
+
+ if (value == null || !(value instanceof ArrayList<?>))
{
return;
}
/*
* if CSQ data includes 'Feature', and any value matches the sequence name,
- * then restrict consequence data to the matching value (transcript)
+ * then restrict consequence data to only the matching value (transcript)
* i.e. just pick out consequences for the transcript the variant feature is on
*/
String seqName = seq.getName()== null ? "" : seq.getName().toLowerCase();
- boolean matchFeature = false;
- String matchFeatureValue = null;
+ String matchFeature = null;
if (csqFeatureFieldIndex > -1)
{
for (String consequence : consequences)
if (featureIdentifier.length() > 4
&& seqName.indexOf(featureIdentifier.toLowerCase()) > -1)
{
- matchFeature = true;
- matchFeatureValue = featureIdentifier;
+ matchFeature = featureIdentifier;
}
}
}
{
String[] csqFields = consequence.split(PIPE_REGEX);
- /*
- * check consequence is for the current transcript
- */
- if (matchFeature)
+ if (includeConsequence(csqFields, matchFeature, variant,
+ altAlelleIndex))
{
- if (csqFields.length <= csqFeatureFieldIndex)
- {
- continue;
- }
- String featureIdentifier = csqFields[csqFeatureFieldIndex];
- if (!featureIdentifier.equals(matchFeatureValue))
+ if (found)
{
- continue; // consequence is for a different transcript
+ sb.append(COMMA);
}
+ found = true;
+ sb.append(consequence);
}
+ }
+
+ if (found)
+ {
+ sf.setValue(CSQ, sb.toString());
+ }
+ }
- if (csqFields.length > csqAlleleNumberFieldIndex)
+ /**
+ * Answers true if we want to associate this block of consequence data with
+ * the specified alternate allele of the VCF variant.
+ * <p>
+ * If consequence data includes the ALLELE_NUM field, then this has to match
+ * altAlleleIndex. Otherwise the Allele field of the consequence data has to
+ * match the allele value.
+ * <p>
+ * Optionally (if matchFeature is not null), restrict to only include
+ * consequences whose Feature value matches. This allows us to attach
+ * consequences to their respective transcripts.
+ *
+ * @param csqFields
+ * @param matchFeature
+ * @param variant
+ * @param altAlelleIndex
+ * (0, 1..)
+ * @return
+ */
+ protected boolean includeConsequence(String[] csqFields,
+ String matchFeature, VariantContext variant, int altAlelleIndex)
+ {
+ /*
+ * check consequence is for the current transcript
+ */
+ if (matchFeature != null)
+ {
+ if (csqFields.length <= csqFeatureFieldIndex)
{
- String alleleNum = csqFields[csqAlleleNumberFieldIndex];
- if (String.valueOf(altAlelleIndex).equals(alleleNum))
- {
- if (found)
- {
- sb.append(COMMA);
- }
- found = true;
- sb.append(consequence);
- }
+ return false;
+ }
+ String featureIdentifier = csqFields[csqFeatureFieldIndex];
+ if (!featureIdentifier.equals(matchFeature))
+ {
+ return false; // consequence is for a different transcript
}
}
- if (found)
+ /*
+ * if ALLELE_NUM is present, it must match altAlleleIndex
+ * NB first alternate allele is 1 for ALLELE_NUM, 0 for altAlleleIndex
+ */
+ if (csqAlleleNumberFieldIndex > -1)
{
- sf.setValue(CSQ, sb.toString());
+ if (csqFields.length <= csqAlleleNumberFieldIndex)
+ {
+ return false;
+ }
+ String alleleNum = csqFields[csqAlleleNumberFieldIndex];
+ return String.valueOf(altAlelleIndex + 1).equals(alleleNum);
}
+
+ /*
+ * else consequence allele must match variant allele
+ */
+ if (csqAlleleFieldIndex > -1 && csqFields.length > csqAlleleFieldIndex)
+ {
+ String csqAllele = csqFields[csqAlleleFieldIndex];
+ String vcfAllele = variant.getAlternateAllele(altAlelleIndex)
+ .getBaseString();
+ return csqAllele.equals(vcfAllele);
+ }
+
+ return false;
}
/**
git://source.jalview.org / jalview.git / commitdiff