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varfish-org · Sep 23, 2023 · 9199f70 · 9199f70
1 parent cad7ef1
commit 9199f70
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Showing 10 changed files with 51 additions and 1 deletion.
diff --git a/Snakefile b/Snakefile
@@ -88,6 +88,7 @@ rule all:
         f"work/download/genes/clingen/{DV.clingen_gene}/clingen.csv",
         f"work/download/genes/rcnv/2022/Collins_rCNV_2022.dosage_sensitivity_scores.tsv.gz",
         f"work/download/genes/orphapacket/{DV.orphapacket}/orphapacket.tar.gz",
+        "work/download/genes/alphamissense/1/AlphaMissense_gene_hg38.tsv.gz",
         f"work/genes/dbnsfp/{DV.dbnsfp}/genes.tsv.gz",
         f"work/genes/ensembl/{DV.ensembl}/ensembl_xlink.tsv",
         f"work/genes/enst_ensg/grch37/{DV.ensembl_37}/enst_ensg.tsv",
@@ -323,6 +324,7 @@ rule all:
 # Misc rules.
 include: "rules/work/misc/hpo.smk"
 # Gene-related rules.
+include: "rules/work/genes/alphamissense.smk"
 include: "rules/work/genes/dbnsfp.smk"
 include: "rules/work/genes/clingen.smk"
 include: "rules/work/genes/ensembl.smk"
@@ -344,6 +346,7 @@ include: "rules/work/annos/features/refseq.smk"
 include: "rules/work/annos/features/tads.smk"
 include: "rules/work/annos/features/ucsc.smk"
 # Sequence variants and annotations.
+include: "rules/work/annos/seqvars/alphamissense.smk"
 include: "rules/work/annos/seqvars/cadd.smk"
 include: "rules/work/annos/seqvars/dbnsfp.smk"
 include: "rules/work/annos/seqvars/dbscsnv.smk"

diff --git a/environment.yml b/environment.yml
@@ -1,4 +1,3 @@
-name: varfish-db-downloader
 channels:
   - bioconda
   - conda-forge

diff --git a/excerpt-data/31296ac84aa243ce/AlphaMissense_hg19.tsv.gz b/excerpt-data/31296ac84aa243ce/AlphaMissense_hg19.tsv.gz
diff --git a/excerpt-data/31296ac84aa243ce/url.txt b/excerpt-data/31296ac84aa243ce/url.txt
diff --git a/excerpt-data/521f5677c9d5d6b3/AlphaMissense_gene_hg38.tsv.gz b/excerpt-data/521f5677c9d5d6b3/AlphaMissense_gene_hg38.tsv.gz
diff --git a/excerpt-data/521f5677c9d5d6b3/url.txt b/excerpt-data/521f5677c9d5d6b3/url.txt
diff --git a/excerpt-data/c47fb6a5c19a1ec2/AlphaMissense_hg38.tsv.gz b/excerpt-data/c47fb6a5c19a1ec2/AlphaMissense_hg38.tsv.gz
diff --git a/excerpt-data/c47fb6a5c19a1ec2/url.txt b/excerpt-data/c47fb6a5c19a1ec2/url.txt
diff --git a/rules/work/annos/seqvars/alphamissense.smk b/rules/work/annos/seqvars/alphamissense.smk
@@ -0,0 +1,15 @@
+## Rules related to the AlphaMissense scores
+
+
+rule annos_alphamissense_download:  # -- download AlphaMissense data
+    output:
+        tsv="work/download/annos/alphamissense/1/{genome}/AlphaMissense_{genome}.tsv.gz",
+        tsv_md5="work/download/annos/alphamissense/1/{genome}/AlphaMissense_{genome}.tsv.gz.md5",
+    shell:
+        r"""
+        wget --no-check-certificate \
+            -O {output.tsv} \
+            https://storage.googleapis.com/dm_alphamissense/AlphaMissense_{wildcards.genome}.tsv.gz
+
+        md5sum {output.tsv} >{output.tsv_md5}
+        """
diff --git a/rules/work/genes/alphamissense.smk b/rules/work/genes/alphamissense.smk
@@ -0,0 +1,15 @@
+## Rules related to AlphaMissense per-gene scores
+
+
+rule genes_alphamissense_download:  # -- download AlphaMissense per-gene scores
+    output:
+        tsv="work/download/genes/alphamissense/1/AlphaMissense_gene_hg38.tsv.gz",
+        tsv_md5="work/download/genes/alphamissense/1/AlphaMissense_gene_hg38.tsv.gz.md5",
+    shell:
+        r"""
+        wget --no-check-certificate \
+            -O {output.tsv} \
+            https://storage.googleapis.com/dm_alphamissense/AlphaMissense_gene_hg38.tsv.gz
+
+        md5sum {output.tsv} > {output.tsv_md5}
+        """