From 504f0822d8572b741bd7b6153299a811cca14367 Mon Sep 17 00:00:00 2001 From: Manuel Holtgrewe Date: Tue, 21 May 2019 12:35:13 +0200 Subject: [PATCH] Fixing HGVS conversion for indels (#452) --- CHANGELOG.md | 1 + .../ProjectTranscriptToChromosome.java | 37 +++--- .../src/main/resources/default_sources.ini | 124 +++++++++--------- .../compbio/jannovar/hgnc/HGNCParser.java | 2 +- 4 files changed, 85 insertions(+), 79 deletions(-) diff --git a/CHANGELOG.md b/CHANGELOG.md index 4d3a5a59a2..52ed5e3d91 100644 --- a/CHANGELOG.md +++ b/CHANGELOG.md @@ -5,6 +5,7 @@ ### jannovar-cli - Using HTTP protocol instead of FTP everywhere as it's possible (#451). +- Fixing HGVS conversion for indels (#452). ## v0.30 diff --git a/jannovar-cli/src/main/java/de/charite/compbio/jannovar/cmd/hgvs_to_vcf/ProjectTranscriptToChromosome.java b/jannovar-cli/src/main/java/de/charite/compbio/jannovar/cmd/hgvs_to_vcf/ProjectTranscriptToChromosome.java index b8975e4eb2..bdae9e96e2 100644 --- a/jannovar-cli/src/main/java/de/charite/compbio/jannovar/cmd/hgvs_to_vcf/ProjectTranscriptToChromosome.java +++ b/jannovar-cli/src/main/java/de/charite/compbio/jannovar/cmd/hgvs_to_vcf/ProjectTranscriptToChromosome.java @@ -13,6 +13,9 @@ import de.charite.compbio.jannovar.hgvs.parser.HGVSParser; import de.charite.compbio.jannovar.hgvs.parser.HGVSParsingException; import de.charite.compbio.jannovar.reference.GenomeVariant; +import de.charite.compbio.jannovar.reference.Strand; +import de.charite.compbio.jannovar.vardbs.base.VariantDescription; +import de.charite.compbio.jannovar.vardbs.base.VariantNormalizer; import htsjdk.samtools.SAMSequenceRecord; import htsjdk.samtools.reference.IndexedFastaSequenceFile; import htsjdk.variant.variantcontext.Allele; @@ -46,6 +49,10 @@ public class ProjectTranscriptToChromosome extends JannovarAnnotationCommand { * Translation of variants */ NucleotideChangeToGenomeVariantTranslator translator; + /** + * Normalization of variants. + */ + VariantNormalizer normalizer; /** * Configuration */ @@ -64,6 +71,7 @@ public void run() throws JannovarException { deserializeTranscriptDefinitionFile(options.getDatabaseFilePath()); System.err.println("Loading FASTA index..."); loadFASTAIndex(); + normalizer = new VariantNormalizer(options.getPathReferenceFASTA()); System.err.println("Opening output VCF file..."); try (VariantContextWriter writer = openOutputFile()) { processFile(writer); @@ -184,7 +192,7 @@ private String mapContigToFasta(String contigName) { // Try to find matching contig in fasta String nameInFasta = null; for (SAMSequenceRecord record : fasta.getSequenceDictionary().getSequences()) { - if (jannovarData.getRefDict().getContigNameToID().containsKey(record.getSequenceName())) { + if (contigID.equals(jannovarData.getRefDict().getContigNameToID().get(record.getSequenceName()))) { nameInFasta = record.getSequenceName(); break; } @@ -196,23 +204,20 @@ private String mapContigToFasta(String contigName) { } private void writeVariant(VariantContextWriter writer, GenomeVariant genomeVar) { - String nameInFasta = mapContigToFasta(genomeVar.getChrName()); - List alleles = new ArrayList(); - int shift = 0; - if (genomeVar.getRef().isEmpty() || genomeVar.getAlt().isEmpty()) { - shift = -1; - String left = fasta.getSubsequenceAt(nameInFasta, genomeVar.getPos(), genomeVar.getPos()) - .getBaseString(); - alleles.add(Allele.create(left + genomeVar.getRef(), true)); - alleles.add(Allele.create(left + genomeVar.getAlt(), false)); - } else { - alleles.add(Allele.create(genomeVar.getRef(), true)); - alleles.add(Allele.create(genomeVar.getAlt(), false)); - } + genomeVar = genomeVar.withStrand(Strand.FWD); + final String nameInFasta = mapContigToFasta(genomeVar.getChrName()); + final VariantDescription desc = normalizer.normalizeInsertion( + new VariantDescription(nameInFasta, genomeVar.getPos(), genomeVar.getRef(), genomeVar.getAlt()) + ); + + final List alleles = Lists.newArrayList( + Allele.create(desc.getRef(), true), + Allele.create(desc.getAlt(), false) + ); VariantContextBuilder builder = new VariantContextBuilder(); - builder.chr(genomeVar.getChrName()).start(genomeVar.getPos() + shift + 1) - .computeEndFromAlleles(alleles, genomeVar.getPos() + shift + 1).alleles(alleles); + builder.chr(nameInFasta).start(desc.getPos() + 1) + .computeEndFromAlleles(alleles, desc.getPos() + 1).alleles(alleles); writer.add(builder.make()); } diff --git a/jannovar-cli/src/main/resources/default_sources.ini b/jannovar-cli/src/main/resources/default_sources.ini index d279a4a6f9..c69795d3d9 100644 --- a/jannovar-cli/src/main/resources/default_sources.ini +++ b/jannovar-cli/src/main/resources/default_sources.ini @@ -54,7 +54,7 @@ type=ucsc alias=MT,M,chrM chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi chrToAccessions.format=chr_NC_gi chrToAccessions.matchLast=HuRef knownCanonical=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/knownCanonical.txt.gz @@ -68,22 +68,22 @@ knownToLocusLink=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/knownTo type=ensembl alias=MT,M,chrM chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi chrToAccessions.format=chr_NC_gi chrToAccessions.matchLast=HuRef -gtf=http://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/Homo_sapiens.NCBI36.54.gtf.gz -cdna=http://ftp.ensembl.org/pub/release-54/fasta/homo_sapiens/cdna/Homo_sapiens.NCBI36.54.cdna.all.fa.gz +gtf=https://ftp.ensembl.org/pub/release-54/gtf/homo_sapiens/Homo_sapiens.NCBI36.54.gtf.gz +cdna=https://ftp.ensembl.org/pub/release-54/fasta/homo_sapiens/cdna/Homo_sapiens.NCBI36.54.cdna.all.fa.gz ; HG18 from RefSeq [hg18/refseq] type=refseq alias=MT,M,chrM chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi chrToAccessions.format=chr_NC_gi chrToAccessions.matchLast=HuRef -gff=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/GFF/ref_NCBI36_top_level.gff3.gz -rna=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/RNA/rna.fa.gz +gff=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/GFF/ref_NCBI36_top_level.gff3.gz +rna=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/RNA/rna.fa.gz ; HG18 from RefSeq (only curated data sets) [hg18/refseq_curated] @@ -91,11 +91,11 @@ type=refseq alias=MT,M,chrM onlyCurated=true chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg18/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/Assembled_chromosomes/chr_NC_gi chrToAccessions.format=chr_NC_gi chrToAccessions.matchLast=HuRef -gff=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/GFF/ref_NCBI36_top_level.gff3.gz -rna=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/RNA/rna.fa.gz +gff=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/GFF/ref_NCBI36_top_level.gff3.gz +rna=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/RNA/rna.fa.gz ; --------------------------------------------------------------------------- ; hg19/GRCh37 @@ -106,7 +106,7 @@ rna=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/BUILD.36.3/RNA/rna.fa. type=ucsc alias=MT,M,chrM chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13 +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13 chrToAccessions.format=chr_accessions knownCanonical=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownCanonical.txt.gz knownGene=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownGene.txt.gz @@ -119,23 +119,23 @@ knownToLocusLink=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/knownTo type=ensembl alias=MT,M,chrM chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13 +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13 chrToAccessions.format=chr_accessions -gtf=http://ftp.ensembl.org/pub/grch37/current/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz -cdna=http://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.cdna.all.fa.gz -table_gene_main=http://ftp.ensembl.org/pub/grch37/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__gene__main.txt.gz.bz2 -table_hgnc=http://ftp.ensembl.org/pub/grch37/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__ox_hgnc__dm.txt.gz.bz2 -table_entrezgene=http://ftp.ensembl.org/pub/grch37/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__ox_entrezgene__dm.txt.gz.bz2 +gtf=https://ftp.ensembl.org/pub/grch37/current/gtf/homo_sapiens/Homo_sapiens.GRCh37.87.gtf.gz +cdna=https://ftp.ensembl.org/pub/grch37/current/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh37.cdna.all.fa.gz +table_gene_main=https://ftp.ensembl.org/pub/grch37/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__gene__main.txt.gz.bz2 +table_hgnc=https://ftp.ensembl.org/pub/grch37/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__ox_hgnc__dm.txt.gz.bz2 +table_entrezgene=https://ftp.ensembl.org/pub/grch37/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__ox_entrezgene__dm.txt.gz.bz2 ; HG19 from RefSeq [hg19/refseq] type=refseq alias=MT,M,chrM chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13 +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13 chrToAccessions.format=chr_accessions -gff=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz -rna=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/RNA/rna.fa.gz +gff=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz +rna=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/RNA/rna.fa.gz ; HG19 from RefSeq (only curated data sets) [hg19/refseq_curated] @@ -143,20 +143,20 @@ type=refseq alias=MT,M,chrM onlyCurated=true chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13 +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13 chrToAccessions.format=chr_accessions -gff=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz -rna=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/RNA/rna.fa.gz +gff=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/GFF/ref_GRCh37.p13_top_level.gff3.gz +rna=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/RNA/rna.fa.gz ; HG19 from RefSeq interim alignment (see https://www.ncbi.nlm.nih.gov/books/NBK430989/#_news_02-14-2017-interim-annotation-update-human_) [hg19/refseq_interim] type=refseq alias=MT,M,chrM chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13 +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13 chrToAccessions.format=chr_accessions -gff=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GRCh37.p13_interim_annotation/interim_GRCh37.p13_top_level_2017-01-13.gff3.gz -rna=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GRCh37.p13_interim_annotation/interim_GRCh37.p13_rna.fa.gz +gff=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GRCh37.p13_interim_annotation/interim_GRCh37.p13_top_level_2017-01-13.gff3.gz +rna=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GRCh37.p13_interim_annotation/interim_GRCh37.p13_rna.fa.gz ; HG19 from RefSeq interim alignment, only curated (see https://www.ncbi.nlm.nih.gov/books/NBK430989/#_news_02-14-2017-interim-annotation-update-human_) [hg19/refseq_interim_curated] @@ -164,10 +164,10 @@ type=refseq alias=MT,M,chrM onlyCurated=true chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg19/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13 +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/ARCHIVE/ANNOTATION_RELEASE.105/Assembled_chromosomes/chr_accessions_GRCh37.p13 chrToAccessions.format=chr_accessions -gff=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GRCh37.p13_interim_annotation/interim_GRCh37.p13_top_level_2017-01-13.gff3.gz -rna=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GRCh37.p13_interim_annotation/interim_GRCh37.p13_rna.fa.gz +gff=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GRCh37.p13_interim_annotation/interim_GRCh37.p13_top_level_2017-01-13.gff3.gz +rna=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GRCh37.p13_interim_annotation/interim_GRCh37.p13_rna.fa.gz ; --------------------------------------------------------------------------- ; hg38/GRCh38 @@ -178,7 +178,7 @@ rna=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GRCh37.p13_interim_annotation/ type=ucsc alias=MT,M,chrM chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/chr_accessions_GRCh38.p12 +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/chr_accessions_GRCh38.p12 chrToAccessions.format=chr_accessions knownCanonical=http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/knownCanonical.txt.gz knownGene=http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/knownGene.txt.gz @@ -191,23 +191,23 @@ knownToLocusLink=http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/knownTo type=ensembl alias=MT,M,chrM chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/chr_accessions_GRCh38.p12 +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/chr_accessions_GRCh38.p12 chrToAccessions.format=chr_accessions -gtf=http://ftp.ensembl.org/pub/release-91/gtf/homo_sapiens/Homo_sapiens.GRCh38.91.gtf.gz -cdna=http://ftp.ensembl.org/pub/release-91/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz -table_gene_main=http://ftp.ensembl.org/pub/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__gene__main.txt.gz -table_hgnc=http://ftp.ensembl.org/pub/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__ox_hgnc__dm.txt.gz -table_entrezgene=http://ftp.ensembl.org/pub/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__ox_entrezgene__dm.txt.gz +gtf=https://ftp.ensembl.org/pub/release-91/gtf/homo_sapiens/Homo_sapiens.GRCh38.91.gtf.gz +cdna=https://ftp.ensembl.org/pub/release-91/fasta/homo_sapiens/cdna/Homo_sapiens.GRCh38.cdna.all.fa.gz +table_gene_main=https://ftp.ensembl.org/pub/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__gene__main.txt.gz +table_hgnc=https://ftp.ensembl.org/pub/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__ox_hgnc__dm.txt.gz +table_entrezgene=https://ftp.ensembl.org/pub/release-95/mysql/ensembl_mart_95/hsapiens_gene_ensembl__ox_entrezgene__dm.txt.gz ; HG38 from RefSeq [hg38/refseq] type=refseq alias=MT,M,chrM chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/chr_accessions_GRCh38.p12 +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/chr_accessions_GRCh38.p12 chrToAccessions.format=chr_accessions -gff=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GFF/ref_GRCh38.p12_top_level.gff3.gz -rna=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/RNA/rna.fa.gz +gff=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GFF/ref_GRCh38.p12_top_level.gff3.gz +rna=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/RNA/rna.fa.gz ; HG38 from RefSeq (only curated data sets) [hg38/refseq_curated] @@ -215,10 +215,10 @@ type=refseq alias=MT,M,chrM onlyCurated=true chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/hg38/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/chr_accessions_GRCh38.p12 +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/Assembled_chromosomes/chr_accessions_GRCh38.p12 chrToAccessions.format=chr_accessions -gff=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GFF/ref_GRCh38.p12_top_level.gff3.gz -rna=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/RNA/rna.fa.gz +gff=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/GFF/ref_GRCh38.p12_top_level.gff3.gz +rna=https://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/RNA/rna.fa.gz ; --------------------------------------------------------------------------- ; mm9 @@ -229,7 +229,7 @@ rna=http://ftp.ncbi.nlm.nih.gov/genomes/H_sapiens/RNA/rna.fa.gz type=ucsc alias=MT,M,chrM chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/Assembled_chromosomes/chr_accessions_MGSCv37 +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/Assembled_chromosomes/chr_accessions_MGSCv37 chrToAccessions.format=chr_accessions knownCanonical=http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/knownCanonical.txt.gz knownGene=http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/knownGene.txt.gz @@ -242,20 +242,20 @@ knownToLocusLink=http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/knownToL type=ensembl alias=MT,M,chrM chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/Assembled_chromosomes/chr_accessions_MGSCv37 +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/Assembled_chromosomes/chr_accessions_MGSCv37 chrToAccessions.format=chr_accessions -gtf=http://ftp.ensembl.org/pub/release-67/gtf/mus_musculus/Mus_musculus.NCBIM37.67.gtf.gz -cdna=http://ftp.ensembl.org/pub/release-67/fasta/mus_musculus/cdna/Mus_musculus.NCBIM37.67.cdna.all.fa.gz +gtf=https://ftp.ensembl.org/pub/release-67/gtf/mus_musculus/Mus_musculus.NCBIM37.67.gtf.gz +cdna=https://ftp.ensembl.org/pub/release-67/fasta/mus_musculus/cdna/Mus_musculus.NCBIM37.67.cdna.all.fa.gz ; MM9 from RefSeq [mm9/refseq] type=refseq alias=MT,M,chrM chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/Assembled_chromosomes/chr_accessions_MGSCv37 +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/Assembled_chromosomes/chr_accessions_MGSCv37 chrToAccessions.format=chr_accessions -gff=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/GFF/ref_MGSCv37_top_level.gff3.gz -rna=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/RNA/rna.fa.gz +gff=https://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/GFF/ref_MGSCv37_top_level.gff3.gz +rna=https://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/RNA/rna.fa.gz ; MM9 from RefSeq (only curated data sets) [mm9/refseq_curated] @@ -263,10 +263,10 @@ type=refseq alias=MT,M,chrM onlyCurated=true chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/mm9/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/Assembled_chromosomes/chr_accessions_MGSCv37 +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/Assembled_chromosomes/chr_accessions_MGSCv37 chrToAccessions.format=chr_accessions -gff=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/GFF/ref_MGSCv37_top_level.gff3.gz -rna=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/RNA/rna.fa.gz +gff=https://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/GFF/ref_MGSCv37_top_level.gff3.gz +rna=https://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/RNA/rna.fa.gz ; --------------------------------------------------------------------------- ; mm10 @@ -277,7 +277,7 @@ rna=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/ARCHIVE/BUILD.37.2/RNA/rna.fa type=ucsc alias=MT,M,chrM chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/Mus_musculus/Assembled_chromosomes/chr_accessions_GRCm38.p4 +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/Mus_musculus/Assembled_chromosomes/chr_accessions_GRCm38.p4 chrToAccessions.format=chr_accessions knownCanonical=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/knownCanonical.txt.gz knownGene=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/knownGene.txt.gz @@ -290,20 +290,20 @@ knownToLocusLink=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/knownTo type=ensembl alias=MT,M,chrM chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/Mus_musculus/Assembled_chromosomes/chr_accessions_GRCm38.p4 +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/Mus_musculus/Assembled_chromosomes/chr_accessions_GRCm38.p4 chrToAccessions.format=chr_accessions -gtf=http://ftp.ensembl.org/pub/release-74/gtf/mus_musculus/Mus_musculus.GRCm38.74.gtf.gz -cdna=http://ftp.ensembl.org/pub/release-74/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.74.cdna.all.fa.gz +gtf=https://ftp.ensembl.org/pub/release-74/gtf/mus_musculus/Mus_musculus.GRCm38.74.gtf.gz +cdna=https://ftp.ensembl.org/pub/release-74/fasta/mus_musculus/cdna/Mus_musculus.GRCm38.74.cdna.all.fa.gz ; MM10 from RefSeq [mm10/refseq] type=refseq alias=MT,M,chrM chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/Mus_musculus/Assembled_chromosomes/chr_accessions_GRCm38.p4 +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/Mus_musculus/Assembled_chromosomes/chr_accessions_GRCm38.p4 chrToAccessions.format=chr_accessions -gff=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/GFF/ref_GRCm38.p4_top_level.gff3.gz -rna=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/RNA/rna.fa.gz +gff=https://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/GFF/ref_GRCm38.p4_top_level.gff3.gz +rna=https://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/RNA/rna.fa.gz ; MM10 from RefSeq (only curated data sets) [mm10/refseq_curated] @@ -311,10 +311,10 @@ type=refseq alias=MT,M,chrM onlyCurated=true chromInfo=http://hgdownload.soe.ucsc.edu/goldenPath/mm10/database/chromInfo.txt.gz -chrToAccessions=http://ftp.ncbi.nlm.nih.gov/genomes/Mus_musculus/Assembled_chromosomes/chr_accessions_GRCm38.p4 +chrToAccessions=https://ftp.ncbi.nlm.nih.gov/genomes/Mus_musculus/Assembled_chromosomes/chr_accessions_GRCm38.p4 chrToAccessions.format=chr_accessions -gff=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/GFF/ref_GRCm38.p4_top_level.gff3.gz -rna=http://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/RNA/rna.fa.gz +gff=https://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/GFF/ref_GRCm38.p4_top_level.gff3.gz +rna=https://ftp.ncbi.nlm.nih.gov/genomes/M_musculus/RNA/rna.fa.gz ; --------------------------------------------------------------------------- ; rn6 diff --git a/jannovar-core/src/main/java/de/charite/compbio/jannovar/hgnc/HGNCParser.java b/jannovar-core/src/main/java/de/charite/compbio/jannovar/hgnc/HGNCParser.java index 2cb1a91c0c..c350a3b008 100644 --- a/jannovar-core/src/main/java/de/charite/compbio/jannovar/hgnc/HGNCParser.java +++ b/jannovar-core/src/main/java/de/charite/compbio/jannovar/hgnc/HGNCParser.java @@ -25,7 +25,7 @@ public class HGNCParser { /** * Download URL for the HGNC complete set TSV file */ - public static final String DOWNLOAD_URL = "ftp://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt"; + public static final String DOWNLOAD_URL = "http://ftp.ebi.ac.uk/pub/databases/genenames/new/tsv/hgnc_complete_set.txt"; /** * Path to the file to parser