X-Git-Url: http://source.jalview.org/gitweb/?a=blobdiff_plain;f=src%2Fjalview%2Fio%2Fvcf%2FVCFLoader.java;h=ac707d8f01cea046948f2809c07256b0739c0ae2;hb=25da4ccb5679905ada8b21e4d21fd416c392ab76;hp=9831af7aa60fe6e27455d84eaba52d888b260c0b;hpb=1b0014839c94c711c09a94641ecb5036072bb5b3;p=jalview.git diff --git a/src/jalview/io/vcf/VCFLoader.java b/src/jalview/io/vcf/VCFLoader.java index 9831af7..ac707d8 100644 --- a/src/jalview/io/vcf/VCFLoader.java +++ b/src/jalview/io/vcf/VCFLoader.java @@ -1,6 +1,5 @@ package jalview.io.vcf; -import jalview.analysis.AlignmentUtils; import jalview.analysis.Dna; import jalview.api.AlignViewControllerGuiI; import jalview.bin.Cache; @@ -23,11 +22,16 @@ import jalview.util.MessageManager; import java.io.File; import java.io.IOException; +import java.io.UnsupportedEncodingException; +import java.net.URLDecoder; import java.util.ArrayList; import java.util.HashMap; +import java.util.HashSet; +import java.util.Iterator; import java.util.List; import java.util.Map; import java.util.Map.Entry; +import java.util.Set; import java.util.regex.Pattern; import java.util.regex.PatternSyntaxException; @@ -35,8 +39,10 @@ import htsjdk.samtools.SAMException; import htsjdk.samtools.SAMSequenceDictionary; import htsjdk.samtools.SAMSequenceRecord; import htsjdk.samtools.util.CloseableIterator; +import htsjdk.tribble.TribbleException; import htsjdk.variant.variantcontext.Allele; import htsjdk.variant.variantcontext.VariantContext; +import htsjdk.variant.vcf.VCFConstants; import htsjdk.variant.vcf.VCFHeader; import htsjdk.variant.vcf.VCFHeaderLine; import htsjdk.variant.vcf.VCFHeaderLineCount; @@ -51,6 +57,31 @@ import htsjdk.variant.vcf.VCFInfoHeaderLine; */ public class VCFLoader { + private static final String ENCODED_COMMA = "%2C"; + + private static final String ENCODED_PERCENT = "%25"; + + private static final String ENCODED_EQUALS = "%3D"; + + private static final String ENCODED_SEMICOLON = "%3B"; + + private static final String ENCODED_COLON = "%3A"; + + private static final String UTF_8 = "UTF-8"; + + /* + * Jalview feature attributes for VCF fixed column data + */ + private static final String VCF_POS = "POS"; + + private static final String VCF_ID = "ID"; + + private static final String VCF_QUAL = "QUAL"; + + private static final String VCF_FILTER = "FILTER"; + + private static final String NO_VALUE = VCFConstants.MISSING_VALUE_v4; // '.' + private static final String DEFAULT_SPECIES = "homo_sapiens"; /** @@ -100,10 +131,12 @@ public class VCFLoader */ private static final String VCF_ASSEMBLY = "VCF_ASSEMBLY"; - private static final String DEFAULT_VCF_ASSEMBLY = "assembly19=GRCh38,hs37=GRCh37,grch37=GRCh37,grch38=GRCh38"; + private static final String DEFAULT_VCF_ASSEMBLY = "assembly19=GRCh37,hs37=GRCh37,grch37=GRCh37,grch38=GRCh38"; private static final String VCF_SPECIES = "VCF_SPECIES"; // default is human + private static final String DEFAULT_REFERENCE = "grch37"; // fallback default is human GRCh37 + /* * keys to fields of VEP CSQ consequence data * see https://www.ensembl.org/info/docs/tools/vep/vep_formats.html @@ -207,6 +240,12 @@ public class VCFLoader */ Map vepFieldsOfInterest; + /* + * key:value for which rejected data has been seen + * (the error is logged only once for each combination) + */ + private Set badData; + /** * Constructor given a VCF file * @@ -263,7 +302,12 @@ public class VCFLoader public SequenceI loadVCFContig(String contig) { VCFHeaderLine headerLine = header.getOtherHeaderLine(VCFHeader.REFERENCE_KEY); - String ref = headerLine == null ? null : headerLine.getValue(); + if (headerLine == null) + { + Cache.log.error("VCF reference header not found"); + return null; + } + String ref = headerLine.getValue(); if (ref.startsWith("file://")) { ref = ref.substring(7); @@ -282,7 +326,7 @@ public class VCFLoader } else { - System.err.println("VCF reference not found: " + ref); + Cache.log.error("VCF reference not found: " + ref); } return seq; @@ -301,7 +345,7 @@ public class VCFLoader { VCFHeaderLine ref = header .getOtherHeaderLine(VCFHeader.REFERENCE_KEY); - String reference = ref.getValue(); + String reference = ref == null ? null : ref.getValue(); setSpeciesAndAssembly(reference); @@ -373,8 +417,13 @@ public class VCFLoader */ protected void setSpeciesAndAssembly(String reference) { + if (reference == null) + { + Cache.log.error("No VCF ##reference found, defaulting to " + + DEFAULT_REFERENCE + ":" + DEFAULT_SPECIES); + reference = DEFAULT_REFERENCE; // default to GRCh37 if not specified + } reference = reference.toLowerCase(); - vcfSpecies = DEFAULT_SPECIES; /* * for a non-human species, or other assembly identifier, @@ -397,6 +446,7 @@ public class VCFLoader } } + vcfSpecies = DEFAULT_SPECIES; prop = Cache.getProperty(VCF_SPECIES); if (prop != null) { @@ -641,7 +691,8 @@ public class VCFLoader /* * dna-to-peptide product mapping */ - AlignmentUtils.computeProteinFeatures(seq, mapTo, map); + // JAL-3187 render on the fly instead + // AlignmentUtils.computeProteinFeatures(seq, mapTo, map); } else { @@ -724,7 +775,7 @@ public class VCFLoader String species = seqCoords.getSpeciesId(); String chromosome = seqCoords.getChromosomeId(); String seqRef = seqCoords.getAssemblyId(); - MapList map = seqCoords.getMap(); + MapList map = seqCoords.getMapping(); // note this requires the configured species to match that // returned with the Ensembl sequence; todo: support aliases? @@ -826,24 +877,35 @@ public class VCFLoader { int vcfStart = Math.min(range[0], range[1]); int vcfEnd = Math.max(range[0], range[1]); - CloseableIterator variants = reader - .query(map.chromosome, vcfStart, vcfEnd); - while (variants.hasNext()) + try { - VariantContext variant = variants.next(); + CloseableIterator variants = reader + .query(map.chromosome, vcfStart, vcfEnd); + while (variants.hasNext()) + { + VariantContext variant = variants.next(); - int[] featureRange = map.map.locateInFrom(variant.getStart(), - variant.getEnd()); + int[] featureRange = map.map.locateInFrom(variant.getStart(), + variant.getEnd()); - if (featureRange != null) - { - int featureStart = Math.min(featureRange[0], featureRange[1]); - int featureEnd = Math.max(featureRange[0], featureRange[1]); - count += addAlleleFeatures(seq, variant, featureStart, featureEnd, - forwardStrand); + if (featureRange != null) + { + int featureStart = Math.min(featureRange[0], featureRange[1]); + int featureEnd = Math.max(featureRange[0], featureRange[1]); + count += addAlleleFeatures(seq, variant, featureStart, + featureEnd, forwardStrand); + } } + variants.close(); + } catch (TribbleException e) + { + /* + * RuntimeException throwable by htsjdk + */ + String msg = String.format("Error reading VCF for %s:%d-%d: %s ", + map.chromosome, vcfStart, vcfEnd); + Cache.log.error(msg); } - variants.close(); } return count; @@ -973,7 +1035,20 @@ public class VCFLoader featureEnd, FEATURE_GROUP_VCF); sf.setSource(sourceId); - sf.setValue(Gff3Helper.ALLELES, alleles); + /* + * save the derived alleles as a named attribute; this will be + * needed when Jalview computes derived peptide variants + */ + addFeatureAttribute(sf, Gff3Helper.ALLELES, alleles); + + /* + * add selected VCF fixed column data as feature attributes + */ + addFeatureAttribute(sf, VCF_POS, String.valueOf(variant.getStart())); + addFeatureAttribute(sf, VCF_ID, variant.getID()); + addFeatureAttribute(sf, VCF_QUAL, + String.valueOf(variant.getPhredScaledQual())); + addFeatureAttribute(sf, VCF_FILTER, getFilter(variant)); addAlleleProperties(variant, sf, altAlleleIndex, consequence); @@ -983,6 +1058,53 @@ public class VCFLoader } /** + * Answers the VCF FILTER value for the variant - or an approximation to it. + * This field is either PASS, or a semi-colon separated list of filters not + * passed. htsjdk saves filters as a HashSet, so the order when reassembled into + * a list may be different. + * + * @param variant + * @return + */ + String getFilter(VariantContext variant) + { + Set filters = variant.getFilters(); + if (filters.isEmpty()) + { + return NO_VALUE; + } + Iterator iterator = filters.iterator(); + String first = iterator.next(); + if (filters.size() == 1) + { + return first; + } + + StringBuilder sb = new StringBuilder(first); + while (iterator.hasNext()) + { + sb.append(";").append(iterator.next()); + } + + return sb.toString(); + } + + /** + * Adds one feature attribute unless the value is null, empty or '.' + * + * @param sf + * @param key + * @param value + */ + void addFeatureAttribute(SequenceFeature sf, String key, String value) + { + if (value != null && !value.isEmpty() && !NO_VALUE.equals(value)) + { + sf.setValue(key, value); + } + } + + /** * 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: @@ -1176,14 +1298,6 @@ public class VCFLoader } /* - * filter out fields we don't want to capture - */ - if (!vcfFieldsOfInterest.contains(key)) - { - continue; - } - - /* * we extract values for other data which are allele-specific; * these may be per alternate allele (INFO[key].Number = 'A') * or per allele including reference (INFO[key].Number = 'R') @@ -1220,14 +1334,110 @@ public class VCFLoader * take the index'th value */ String value = getAttributeValue(variant, key, index); - if (value != null) + if (value != null && isValid(variant, key, value)) { - sf.setValue(key, value); + value = decodeSpecialCharacters(value); + addFeatureAttribute(sf, key, value); } } } /** + * Decodes colon, semicolon, equals sign, percent sign, comma to their decoded + * form. The VCF specification (para 1.2) requires these to be encoded where not + * used with their special meaning in the VCF syntax. Note that general URL + * decoding should not be applied, since this would incorrectly decode (for + * example) a '+' sign. + * + * @param value + * @return + */ + protected static String decodeSpecialCharacters(String value) + { + /* + * avoid regex compilation if it is not needed! + */ + if (!value.contains(ENCODED_COLON) && !value.contains(ENCODED_SEMICOLON) + && !value.contains(ENCODED_EQUALS) + && !value.contains(ENCODED_PERCENT) + && !value.contains(ENCODED_COMMA)) + { + return value; + } + + value = value.replace(ENCODED_COLON, ":") + .replace(ENCODED_SEMICOLON, ";").replace(ENCODED_EQUALS, "=") + .replace(ENCODED_PERCENT, "%").replace(ENCODED_COMMA, ","); + return value; + } + + /** + * Answers true for '.', null, or an empty value, or if the INFO type is String. + * If the INFO type is Integer or Float, answers false if the value is not in + * valid format. + * + * @param variant + * @param infoId + * @param value + * @return + */ + protected boolean isValid(VariantContext variant, String infoId, + String value) + { + if (value == null || value.isEmpty() || NO_VALUE.equals(value)) + { + return true; + } + VCFInfoHeaderLine infoHeader = header.getInfoHeaderLine(infoId); + if (infoHeader == null) + { + Cache.log.error("Field " + infoId + " has no INFO header"); + return false; + } + VCFHeaderLineType infoType = infoHeader.getType(); + try + { + if (infoType == VCFHeaderLineType.Integer) + { + Integer.parseInt(value); + } + else if (infoType == VCFHeaderLineType.Float) + { + Float.parseFloat(value); + } + } catch (NumberFormatException e) + { + logInvalidValue(variant, infoId, value); + return false; + } + return true; + } + + /** + * Logs an error message for malformed data; duplicate messages (same id and + * value) are not logged + * + * @param variant + * @param infoId + * @param value + */ + private void logInvalidValue(VariantContext variant, String infoId, + String value) + { + if (badData == null) + { + badData = new HashSet<>(); + } + String token = infoId + ":" + value; + if (!badData.contains(token)) + { + badData.add(token); + Cache.log.error(String.format("Invalid VCF data at %s:%d %s=%s", + variant.getContig(), variant.getStart(), infoId, value)); + } + } + + /** * Inspects CSQ data blocks (consequences) and adds attributes on the sequence * feature. *

@@ -1275,6 +1485,16 @@ public class VCFLoader String id = vepFieldsOfInterest.get(i); if (id != null) { + /* + * VCF spec requires encoding of special characters e.g. '=' + * so decode them here before storing + */ + try + { + field = URLDecoder.decode(field, UTF_8); + } catch (UnsupportedEncodingException e) + { + } csqValues.put(id, field); } }