Issue #1101 - Update settings.ANNOTATION to latest

SACGF · Jul 8, 2024 · de5dfe0 · de5dfe0
1 parent 7e2ca32
commit de5dfe0
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Showing 5 changed files with 22 additions and 64 deletions.
diff --git 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
@@ -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
@@ -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
@@ -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
@@ -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')