From de5dfe0c961603f5cb4b23a7e54121e600931b4e Mon Sep 17 00:00:00 2001 From: Dave Lawrence Date: Mon, 8 Jul 2024 13:27:39 +0930 Subject: [PATCH] Issue #1101 - Update settings.ANNOTATION to latest --- .../settings/components/default_settings.py | 16 ++++++------- variantgrid/settings/env/runx1db2.py | 8 +++++++ variantgrid/settings/env/shariantcommon.py | 20 ++++------------ variantgrid/settings/env/vgaws.py | 23 +------------------ variantgrid/settings/env/vgtest.py | 19 --------------- 5 files changed, 22 insertions(+), 64 deletions(-) diff --git a/variantgrid/settings/components/default_settings.py b/variantgrid/settings/components/default_settings.py index 9cdfd5a3b..d4f7702f5 100644 --- a/variantgrid/settings/components/default_settings.py +++ b/variantgrid/settings/components/default_settings.py @@ -231,7 +231,7 @@ BUILD_GRCH37: { "enabled": True, "annotation_consortium": "Ensembl", - "columns_version": 1, + "columns_version": 3, "cytoband": os.path.join(VG_REFERENCE_DIR, "hg19", "cytoband.hg19.txt.gz"), "reference_fasta": os.path.join(_ANNOTATION_FASTA_BASE_DIR, "GCF_000001405.25_GRCh37.p13_genomic.fna.gz"), "reference_fasta_has_chr": False, @@ -243,15 +243,15 @@ # so you can change just that variable and have everything else work # The names correspond to VEPPlugin or VEPCustom entries (but lower case) "vep_config": { - "cosmic": "annotation_data/GRCh37/CosmicCodingMuts_v95_20211101_grch37.normal.vcf.gz", - "dbnsfp": "annotation_data/GRCh37/dbNSFP4.0a.grch37.stripped.gz", + "cosmic": "annotation_data/GRCh37/Cosmic_GenomeScreensMutant_v99_GRCh37.vcf.gz", + "dbnsfp": "annotation_data/GRCh37/dbNSFP4.5a.grch37.stripped.gz", "dbscsnv": "annotation_data/GRCh37/dbscSNV1.1_GRCh37.txt.gz", "gnomad2": "annotation_data/GRCh37/gnomad2.1.1_GRCh37_combined_af.vcf.bgz", # We use gnomAD SV VCF with --custom twice "gnomad_sv": "annotation_data/GRCh37/gnomad_v2.1_sv.sites.grch37.converted.no_filters.vcf.gz", "gnomad_sv_name": "annotation_data/GRCh37/gnomad_v2.1_sv.sites.grch37.converted.no_filters.vcf.gz", "fasta": os.path.join(_ANNOTATION_FASTA_BASE_DIR, "Homo_sapiens.GRCh37.75.dna.primary_assembly.fa.gz"), - "mastermind": "annotation_data/GRCh37/mastermind_cited_variants_reference-2022.04.02-grch37.vcf.gz", + "mastermind": "annotation_data/GRCh37/mastermind_cited_variants_reference-2023.10.02-grch37.vcf.gz", "mave": None, # n/a for GRCh37 "maxentscan": "annotation_data/all_builds/maxentscan", 'phastcons100way': "annotation_data/GRCh37/hg19.100way.phastCons.bw", @@ -271,7 +271,7 @@ BUILD_GRCH38: { "enabled": False, "annotation_consortium": "Ensembl", - "columns_version": 1, + "columns_version": 3, "cytoband": os.path.join(VG_REFERENCE_DIR, "hg38", "cytoband.hg38.txt.gz"), "reference_fasta": os.path.join(_ANNOTATION_FASTA_BASE_DIR, "GCF_000001405.39_GRCh38.p13_genomic.fna.gz"), "reference_fasta_has_chr": False, @@ -283,8 +283,8 @@ # so you can change just that variable and have everything else work # The names correspond to VEPPlugin or VEPCustom entries (but lower case) "vep_config": { - "cosmic": "annotation_data/GRCh38/CosmicCodingMuts_v95_20211101_grch38.normal.vcf.gz", - "dbnsfp": "annotation_data/GRCh38/dbNSFP4.0a.grch38.stripped.gz", + "cosmic": "annotation_data/GRCh38/Cosmic_GenomeScreensMutant_v99_GRCh38.vcf.gz", + "dbnsfp": "annotation_data/GRCh38/dbNSFP4.5a.grch38.stripped.gz", "dbscsnv": "annotation_data/GRCh38/dbscSNV1.1_GRCh38.txt.gz", "fasta": os.path.join(_ANNOTATION_FASTA_BASE_DIR, "Homo_sapiens.GRCh38.dna.toplevel.fa.gz"), "gnomad2": "annotation_data/GRCh38/gnomad2.1.1_GRCh38_combined_af.vcf.bgz", @@ -293,7 +293,7 @@ # We use gnomAD SV VCF with --custom twice "gnomad_sv": "annotation_data/GRCh38/gnomad.v4.0.sv.merged.no_filters.vcf.gz", "gnomad_sv_name": "annotation_data/GRCh38/gnomad.v4.0.sv.merged.no_filters.vcf.gz", - "mastermind": "annotation_data/GRCh38/mastermind_cited_variants_reference-2022.04.02-grch38.vcf.gz", + "mastermind": "annotation_data/GRCh38/mastermind_cited_variants_reference-2023.10.02-grch38.vcf.gz", "mave": "annotation_data/GRCh38/MaveDB_variants.tsv.gz", "maxentscan": "annotation_data/all_builds/maxentscan", 'phastcons100way': "annotation_data/GRCh38/hg38.phastCons100way.bw", diff --git a/variantgrid/settings/env/runx1db2.py b/variantgrid/settings/env/runx1db2.py index 30feeb5b0..193eb1c88 100644 --- a/variantgrid/settings/env/runx1db2.py +++ b/variantgrid/settings/env/runx1db2.py @@ -27,9 +27,17 @@ _ANNOTATION_FASTA_BASE_DIR = os.path.join(ANNOTATION_BASE_DIR, "fasta") ANNOTATION[BUILD_GRCH37].update({ + "columns_version": 1, "reference_fasta": os.path.join(_ANNOTATION_FASTA_BASE_DIR, "GCF_000001405.25_GRCh37.p13_genomic.fna.gz"), }) +ANNOTATION[BUILD_GRCH37]["vep_config"].update({ + "cosmic": "annotation_data/GRCh37/CosmicCodingMuts_v95_20211101_grch37.normal.vcf.gz", + "dbnsfp": "annotation_data/GRCh37/dbNSFP4.0a.grch37.stripped.gz", + "mastermind": "annotation_data/GRCh37/mastermind_cited_variants_reference-2022.04.02-grch37.vcf.gz", +}) + + GENES_DEFAULT_CANONICAL_TRANSCRIPT_COLLECTION_ID = 1 # MedEx PATIENTS_READ_ONLY_SHOW_AGE_NOT_DOB = True diff --git a/variantgrid/settings/env/shariantcommon.py b/variantgrid/settings/env/shariantcommon.py index df4781c00..4a828ba8a 100644 --- a/variantgrid/settings/env/shariantcommon.py +++ b/variantgrid/settings/env/shariantcommon.py @@ -117,22 +117,12 @@ ANNOTATION_VCF_DUMP_DIR = os.path.join(_ANNOTATION_BASE_DIR, 'annotation_scratch') ANNOTATION_VEP_PERLBREW_RUNNER_SCRIPT = os.path.join(BASE_DIR, "scripts", "perlbrew_runner.sh") -ANNOTATION[BUILD_GRCH37]["enabled"] = True -ANNOTATION[BUILD_GRCH37]["annotation_consortium"] = "RefSeq" -ANNOTATION[BUILD_GRCH37]["columns_version"] = 3 -ANNOTATION[BUILD_GRCH37]["vep_config"].update({ - "cosmic": "annotation_data/GRCh37/Cosmic_GenomeScreensMutant_v99_GRCh37.vcf.gz", - "dbnsfp": "annotation_data/GRCh37/dbNSFP4.5a.grch37.stripped.gz", - "mastermind": "annotation_data/GRCh37/mastermind_cited_variants_reference-2023.10.02-grch37.vcf.gz", +ANNOTATION[BUILD_GRCH37].update({ + "annotation_consortium": "RefSeq", }) - -ANNOTATION[BUILD_GRCH38]["enabled"] = True -ANNOTATION[BUILD_GRCH38]["annotation_consortium"] = "RefSeq" -ANNOTATION[BUILD_GRCH38]["columns_version"] = 3 -ANNOTATION[BUILD_GRCH38]["vep_config"].update({ - "cosmic": "annotation_data/GRCh38/Cosmic_GenomeScreensMutant_v99_GRCh38.vcf.gz", - "dbnsfp": "annotation_data/GRCh38/dbNSFP4.5a.grch38.stripped.gz", - "mastermind": "annotation_data/GRCh38/mastermind_cited_variants_reference-2023.10.02-grch38.vcf.gz", +ANNOTATION[BUILD_GRCH38].update({ + "enabled": True, + "annotation_consortium": "RefSeq", }) LOGIN_REDIRECT_URL = '/classification/dashboard' diff --git a/variantgrid/settings/env/vgaws.py b/variantgrid/settings/env/vgaws.py index e1c5eebe3..00a23895d 100644 --- a/variantgrid/settings/env/vgaws.py +++ b/variantgrid/settings/env/vgaws.py @@ -28,28 +28,7 @@ ANNOTATION_VEP_PERLBREW_RUNNER_SCRIPT = os.path.expanduser("~/perlbrew_runner.sh") _ANNOTATION_FASTA_BASE_DIR = os.path.join(ANNOTATION_REFERENCE_BASE_DIR, "fasta") -ANNOTATION[BUILD_GRCH37].update({ - "columns_version": 3, - "reference_fasta": os.path.join(_ANNOTATION_FASTA_BASE_DIR, "GCF_000001405.25_GRCh37.p13_genomic.fna.gz"), -}) - -ANNOTATION[BUILD_GRCH38].update({ - "columns_version": 3, - "enabled": True, - "reference_fasta": os.path.join(_ANNOTATION_FASTA_BASE_DIR, "GCF_000001405.39_GRCh38.p13_genomic.fna.gz"), -}) - -ANNOTATION[BUILD_GRCH37]["vep_config"].update({ - "cosmic": "annotation_data/GRCh37/Cosmic_GenomeScreensMutant_v99_GRCh37.vcf.gz", - "dbnsfp": "annotation_data/GRCh37/dbNSFP4.5a.grch37.stripped.gz", - "mastermind": "annotation_data/GRCh37/mastermind_cited_variants_reference-2023.10.02-grch37.vcf.gz", -}) -ANNOTATION[BUILD_GRCH38]["vep_config"].update({ - "cosmic": "annotation_data/GRCh38/Cosmic_GenomeScreensMutant_v99_GRCh38.vcf.gz", - "dbnsfp": "annotation_data/GRCh38/dbNSFP4.5a.grch38.stripped.gz", - "mastermind": "annotation_data/GRCh38/mastermind_cited_variants_reference-2023.10.02-grch38.vcf.gz", -}) - +ANNOTATION[BUILD_GRCH38]["enabled"] = True ANNOTATION_VCF_DUMP_DIR = os.path.join(_BIG_DISK_BASE_DIR, 'annotation_scratch') GENES_DEFAULT_CANONICAL_TRANSCRIPT_COLLECTION_ID = 1 # MedEx diff --git a/variantgrid/settings/env/vgtest.py b/variantgrid/settings/env/vgtest.py index 92a73d849..735d0ccf4 100644 --- a/variantgrid/settings/env/vgtest.py +++ b/variantgrid/settings/env/vgtest.py @@ -25,27 +25,8 @@ MANAGE_COMMAND = [PYTHON_COMMAND, os.path.join(BASE_DIR, "manage.py")] -ANNOTATION[BUILD_GRCH37].update({ - "columns_version": 3, - "reference_fasta": os.path.join(_ANNOTATION_FASTA_BASE_DIR, "GCF_000001405.25_GRCh37.p13_genomic.fna.gz"), -}) - ANNOTATION[BUILD_GRCH38].update({ - "columns_version": 3, "enabled": True, - "reference_fasta": os.path.join(_ANNOTATION_FASTA_BASE_DIR, "GCF_000001405.39_GRCh38.p13_genomic.fna.gz"), -}) - - -ANNOTATION[BUILD_GRCH37]["vep_config"].update({ - "cosmic": "annotation_data/GRCh37/Cosmic_GenomeScreensMutant_v99_GRCh37.vcf.gz", - "dbnsfp": "annotation_data/GRCh37/dbNSFP4.5a.grch37.stripped.gz", - "mastermind": "annotation_data/GRCh37/mastermind_cited_variants_reference-2023.10.02-grch37.vcf.gz", -}) -ANNOTATION[BUILD_GRCH38]["vep_config"].update({ - "cosmic": "annotation_data/GRCh38/Cosmic_GenomeScreensMutant_v99_GRCh38.vcf.gz", - "dbnsfp": "annotation_data/GRCh38/dbNSFP4.5a.grch38.stripped.gz", - "mastermind": "annotation_data/GRCh38/mastermind_cited_variants_reference-2023.10.02-grch38.vcf.gz", }) ANNOTATION_VCF_DUMP_DIR = os.path.join(ANNOTATION_BASE_DIR, 'scratch')