import java.util.List;
import java.util.Map;
import java.util.Map.Entry;
-import java.util.SortedMap;
-import java.util.TreeMap;
import java.util.regex.Pattern;
import java.util.regex.PatternSyntaxException;
chromosome = chr;
map = m;
}
+
+ @Override
+ public String toString()
+ {
+ return chromosome + ":" + map.toString();
+ }
}
/*
* 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_KEY = "Allele";
-
- private static final String ALLELE_NUM_KEY = "ALLELE_NUM"; // 0 (ref), 1...
- private static final String FEATURE_KEY = "Feature"; // Ensembl stable id
+ private static final String CSQ_CONSEQUENCE_KEY = "Consequence";
+ private static final String CSQ_ALLELE_KEY = "Allele";
+ private static final String CSQ_ALLELE_NUM_KEY = "ALLELE_NUM"; // 0 (ref), 1...
+ private static final String CSQ_FEATURE_KEY = "Feature"; // Ensembl stable id
/*
* default VCF INFO key for VEP consequence data
* 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 csqConsequenceFieldIndex = -1;
private int csqAlleleFieldIndex = -1;
private int csqAlleleNumberFieldIndex = -1;
private int csqFeatureFieldIndex = -1;
+ // todo the same fields for SnpEff ANN data if wanted
+ // see http://snpeff.sourceforge.net/SnpEff_manual.html#input
+
/*
* a unique identifier under which to save metadata about feature
* attributes (selected INFO field data)
int index = 0;
for (String field : format)
{
- if (ALLELE_NUM_KEY.equals(field))
+ if (CSQ_CONSEQUENCE_KEY.equals(field))
+ {
+ csqConsequenceFieldIndex = index;
+ }
+ if (CSQ_ALLELE_NUM_KEY.equals(field))
{
csqAlleleNumberFieldIndex = index;
}
- if (ALLELE_KEY.equals(field))
+ if (CSQ_ALLELE_KEY.equals(field))
{
csqAlleleFieldIndex = index;
}
- if (FEATURE_KEY.equals(field))
+ if (CSQ_FEATURE_KEY.equals(field))
{
csqFeatureFieldIndex = index;
}
/**
* Inspects one allele and attempts to add a variant feature for it to the
- * 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).
+ * sequence. The additional data associated with this allele is extracted to
+ * store in the feature's key-value map. Answers the number of features added (0
+ * or 1).
*
* @param seq
* @param variant
* 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
+ // FIXME correctly handle insertions on reverse strand JAL-2845
StringBuilder sb = new StringBuilder();
sb.append(forwardStrand ? reference : Dna.reverseComplement(reference));
sb.append(COMMA);
sb.append(forwardStrand ? allele : Dna.reverseComplement(allele));
String alleles = sb.toString(); // e.g. G,A
- String type = SequenceOntologyI.SEQUENCE_VARIANT;
+ String type = getOntologyTerm(seq, variant, altAlleleIndex);
+
float score = getAlleleFrequency(variant, altAlleleIndex);
SequenceFeature sf = new SequenceFeature(type, alleles, featureStart,
}
/**
+ * Determines the Sequence Ontology term to use for the variant feature type in
+ * Jalview. The default is 'sequence_variant', but a more specific term is used
+ * if:
+ * <ul>
+ * <li>VEP (or SnpEff) Consequence annotation is included in the VCF</li>
+ * <li>sequence id can be matched to VEP Feature (or SnpEff Feature_ID)</li>
+ * </ul>
+ *
+ * @param seq
+ * @param variant
+ * @param altAlleleIndex
+ * @return
+ * @see http://www.sequenceontology.org/browser/current_svn/term/SO:0001060
+ */
+ String getOntologyTerm(SequenceI seq, VariantContext variant,
+ int altAlleleIndex)
+ {
+ String type = SequenceOntologyI.SEQUENCE_VARIANT;
+
+ if (csqAlleleFieldIndex == -1) // && snpEffAlleleFieldIndex == -1
+ {
+ /*
+ * no Consequence data so we can't refine the ontology term
+ */
+ return type;
+ }
+
+ /*
+ * can we associate Consequence data with this allele and feature (transcript)?
+ * if so, prefer the consequence term from that data
+ */
+ String consequence = getConsequenceForAlleleAndFeature(variant,
+ CSQ_FIELD,
+ altAlleleIndex, csqAlleleFieldIndex, csqAlleleNumberFieldIndex,
+ seq.getName().toLowerCase(), csqFeatureFieldIndex);
+ if (consequence != null)
+ {
+ String[] csqFields = consequence.split(PIPE_REGEX);
+ if (csqFields.length > csqConsequenceFieldIndex)
+ {
+ type = csqFields[csqConsequenceFieldIndex];
+ }
+ }
+ else
+ {
+ // todo the same for SnpEff consequence data matching if wanted
+ }
+
+ /*
+ * if of the form (e.g.) missense_variant&splice_region_variant,
+ * just take the first ('most severe') consequence
+ */
+ if (type != null)
+ {
+ int pos = type.indexOf('&');
+ if (pos > 0)
+ {
+ type = type.substring(0, pos);
+ }
+ }
+ return type;
+ }
+
+ /**
+ * Returns matched consequence data if it can be found, else null.
+ * <ul>
+ * <li>inspects the VCF data for key 'vcfInfoId'</li>
+ * <li>splits this on comma (to distinct consequences)</li>
+ * <li>returns the first consequence (if any) where</li>
+ * <ul>
+ * <li>the allele matches the altAlleleIndex'th allele of variant</li>
+ * <li>the feature matches the sequence name (e.g. transcript id)</li>
+ * </ul>
+ * </ul>
+ * If matched, the consequence is returned (as pipe-delimited fields).
+ *
+ * @param variant
+ * @param vcfInfoId
+ * @param altAlleleIndex
+ * @param alleleFieldIndex
+ * @param alleleNumberFieldIndex
+ * @param seqName
+ * @param featureFieldIndex
+ * @return
+ */
+ private String getConsequenceForAlleleAndFeature(VariantContext variant,
+ String vcfInfoId, int altAlleleIndex, int alleleFieldIndex,
+ int alleleNumberFieldIndex,
+ String seqName, int featureFieldIndex)
+ {
+ if (alleleFieldIndex == -1 || featureFieldIndex == -1)
+ {
+ return null;
+ }
+ Object value = variant.getAttribute(vcfInfoId);
+
+ if (value == null || !(value instanceof List<?>))
+ {
+ return null;
+ }
+
+ /*
+ * inspect each consequence in turn (comma-separated blocks
+ * extracted by htsjdk)
+ */
+ List<String> consequences = (List<String>) value;
+
+ for (String consequence : consequences)
+ {
+ String[] csqFields = consequence.split(PIPE_REGEX);
+ if (csqFields.length > featureFieldIndex)
+ {
+ String featureIdentifier = csqFields[featureFieldIndex];
+ if (featureIdentifier.length() > 4
+ && seqName.indexOf(featureIdentifier.toLowerCase()) > -1)
+ {
+ /*
+ * feature (transcript) matched - now check for allele match
+ */
+ if (matchAllele(variant, altAlleleIndex, csqFields,
+ alleleFieldIndex, alleleNumberFieldIndex))
+ {
+ return consequence;
+ }
+ }
+ }
+ }
+ return null;
+ }
+
+ private boolean matchAllele(VariantContext variant, int altAlleleIndex,
+ String[] csqFields, int alleleFieldIndex,
+ int alleleNumberFieldIndex)
+ {
+ /*
+ * if ALLELE_NUM is present, it must match altAlleleIndex
+ * NB first alternate allele is 1 for ALLELE_NUM, 0 for altAlleleIndex
+ */
+ if (alleleNumberFieldIndex > -1)
+ {
+ if (csqFields.length <= alleleNumberFieldIndex)
+ {
+ return false;
+ }
+ String alleleNum = csqFields[alleleNumberFieldIndex];
+ return String.valueOf(altAlleleIndex + 1).equals(alleleNum);
+ }
+
+ /*
+ * else consequence allele must match variant allele
+ */
+ if (alleleFieldIndex > -1 && csqFields.length > alleleFieldIndex)
+ {
+ String csqAllele = csqFields[alleleFieldIndex];
+ String vcfAllele = variant.getAlternateAllele(altAlleleIndex)
+ .getBaseString();
+ return csqAllele.equals(vcfAllele);
+ }
+ return false;
+ }
+
+ /**
* Add any allele-specific VCF key-value data to the sequence feature
*
* @param variant
* @param variant
* @param seq
* @param sf
- * @param altAlelleIndex
+ * @param altAlleleIndex
* (0, 1..)
*/
protected void addConsequences(VariantContext variant, SequenceI seq,
- SequenceFeature sf, int altAlelleIndex)
+ SequenceFeature sf, int altAlleleIndex)
{
+ /*
+ * first try to identify the matching consequence
+ */
+ String myConsequence = getConsequenceForAlleleAndFeature(variant,
+ CSQ_FIELD, altAlleleIndex, csqAlleleFieldIndex,
+ csqAlleleNumberFieldIndex, seq.getName().toLowerCase(),
+ csqFeatureFieldIndex);
+
Object value = variant.getAttribute(CSQ_FIELD);
- if (value == null || !(value instanceof ArrayList<?>))
+ if (value == null || !(value instanceof List<?>))
{
return;
}
List<String> consequences = (List<String>) value;
/*
- * if CSQ data includes 'Feature', and any value matches the sequence name,
- * 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();
- String matchFeature = null;
- if (csqFeatureFieldIndex > -1)
- {
- for (String consequence : consequences)
- {
- String[] csqFields = consequence.split(PIPE_REGEX);
- if (csqFields.length > csqFeatureFieldIndex)
- {
- String featureIdentifier = csqFields[csqFeatureFieldIndex];
- if (featureIdentifier.length() > 4
- && seqName.indexOf(featureIdentifier.toLowerCase()) > -1)
- {
- matchFeature = featureIdentifier;
- }
- }
- }
- }
-
- /*
- * inspect CSQ consequences; where possible restrict to the consequence
+ * inspect CSQ consequences; restrict to the consequence
* associated with the current transcript (Feature)
*/
- SortedMap<String, String> csqValues = new TreeMap<>(
- String.CASE_INSENSITIVE_ORDER);
+ Map<String, String> csqValues = new HashMap<>();
for (String consequence : consequences)
{
- String[] csqFields = consequence.split(PIPE_REGEX);
-
- if (includeConsequence(csqFields, matchFeature, variant,
- altAlelleIndex))
+ if (myConsequence == null || myConsequence.equals(consequence))
{
+ String[] csqFields = consequence.split(PIPE_REGEX);
+
/*
* inspect individual fields of this consequence, copying non-null
* values which are 'fields of interest'
}
/**
- * 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)
- {
- return false;
- }
- String featureIdentifier = csqFields[csqFeatureFieldIndex];
- if (!featureIdentifier.equals(matchFeature))
- {
- return false; // consequence is for a different transcript
- }
- }
-
- /*
- * if ALLELE_NUM is present, it must match altAlleleIndex
- * NB first alternate allele is 1 for ALLELE_NUM, 0 for altAlleleIndex
- */
- if (csqAlleleNumberFieldIndex > -1)
- {
- 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;
- }
-
- /**
* A convenience method to complement a dna base and return the string value
* of its complement
*
git://source.jalview.org / jalview.git / commitdiff