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varfish-org · Jul 14, 2024 · d1646e2 · d1646e2
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commit d1646e2
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diff --git a/Snakefile b/Snakefile
@@ -213,7 +213,6 @@ rule all:
         f"output/full/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype.hpoa",
         f"output/full/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype_to_genes.txt",
         f"output/full/viguno/hpo-{DV.hpo}+{PV.viguno}/hpo.bin",
-        f"output/full/viguno/hpo-{DV.hpo}+{PV.viguno}/scores-fun-sim-avg-resnik-gene/IDENTITY",
         # ----- background/population structural variants and annotations thereof
         f"output/full/tracks/track-strucvars-dbvar-grch37-{DV.dbvar}+{DV.tracks}/dbvar.bed.gz",
         f"output/full/tracks/track-strucvars-dbvar-grch38-{DV.dbvar}+{DV.tracks}/dbvar.bed.gz",
@@ -275,7 +274,6 @@ rule all:
         f"output/reduced-dev/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype.hpoa",
         f"output/reduced-dev/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype_to_genes.txt",
         f"output/reduced-dev/viguno/hpo-{DV.hpo}+{PV.viguno}/hpo.bin",
-        f"output/reduced-dev/viguno/hpo-{DV.hpo}+{PV.viguno}/scores-fun-sim-avg-resnik-gene/IDENTITY",
         # -- annonars
         f"output/reduced-dev/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/reduced-dev/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
@@ -307,7 +305,6 @@ rule all:
         f"output/reduced-exomes/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype.hpoa",
         f"output/reduced-exomes/viguno/hpo-{DV.hpo}+{PV.viguno}/phenotype_to_genes.txt",
         f"output/reduced-exomes/viguno/hpo-{DV.hpo}+{PV.viguno}/hpo.bin",
-        f"output/reduced-exomes/viguno/hpo-{DV.hpo}+{PV.viguno}/scores-fun-sim-avg-resnik-gene/IDENTITY",
         # -- annonars
         f"output/reduced-exomes/annonars/cadd-grch37-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",
         f"output/reduced-exomes/annonars/cadd-grch38-{DV.cadd}+{PV.annonars}/rocksdb/IDENTITY",

diff --git a/rules/reduced/hpo.smk b/rules/reduced/hpo.smk
@@ -8,14 +8,12 @@ rule subset_viguno_pheno_exomes:  # -- create exomes subset
         obo="output/full/viguno/hpo-{v_hpo}+{v_viguno}/hp.obo",
         hpoa="output/full/viguno/hpo-{v_hpo}+{v_viguno}/phenotype.hpoa",
         phenotype_to_genes="output/full/viguno/hpo-{v_hpo}+{v_viguno}/phenotype_to_genes.txt",
-        rocksdb_identity="output/full/viguno/hpo-{v_hpo}+{v_viguno}/scores-fun-sim-avg-resnik-gene/IDENTITY",
         bin="output/full/viguno/hpo-{v_hpo}+{v_viguno}/hpo.bin",
         spec_yaml="output/full/viguno/hpo-{v_hpo}+{v_viguno}/spec.yaml",
     output:
         obo="output/reduced-exomes/viguno/hpo-{v_hpo}+{v_viguno}/hp.obo",
         hpoa="output/reduced-exomes/viguno/hpo-{v_hpo}+{v_viguno}/phenotype.hpoa",
         phenotype_to_genes="output/reduced-exomes/viguno/hpo-{v_hpo}+{v_viguno}/phenotype_to_genes.txt",
-        rocksdb_identity="output/reduced-exomes/viguno/hpo-{v_hpo}+{v_viguno}/scores-fun-sim-avg-resnik-gene/IDENTITY",
         bin="output/reduced-exomes/viguno/hpo-{v_hpo}+{v_viguno}/hpo.bin",
         spec_yaml="output/reduced-exomes/viguno/hpo-{v_hpo}+{v_viguno}/spec.yaml",
     wildcard_constraints:
@@ -38,14 +36,12 @@ rule subset_worker_pheno_dev:  # -- create development subset
         obo="output/full/viguno/hpo-{v_hpo}+{v_viguno}/hp.obo",
         hpoa="output/full/viguno/hpo-{v_hpo}+{v_viguno}/phenotype.hpoa",
         phenotype_to_genes="output/full/viguno/hpo-{v_hpo}+{v_viguno}/phenotype_to_genes.txt",
-        rocksdb_identity="output/full/viguno/hpo-{v_hpo}+{v_viguno}/scores-fun-sim-avg-resnik-gene/IDENTITY",
         bin="output/full/viguno/hpo-{v_hpo}+{v_viguno}/hpo.bin",
         spec_yaml="output/full/viguno/hpo-{v_hpo}+{v_viguno}/spec.yaml",
     output:
         obo="output/reduced-dev/viguno/hpo-{v_hpo}+{v_viguno}/hp.obo",
         hpoa="output/reduced-dev/viguno/hpo-{v_hpo}+{v_viguno}/phenotype.hpoa",
         phenotype_to_genes="output/reduced-dev/viguno/hpo-{v_hpo}+{v_viguno}/phenotype_to_genes.txt",
-        rocksdb_identity="output/reduced-dev/viguno/hpo-{v_hpo}+{v_viguno}/scores-fun-sim-avg-resnik-gene/IDENTITY",
         bin="output/reduced-dev/viguno/hpo-{v_hpo}+{v_viguno}/hpo.bin",
         spec_yaml="output/reduced-dev/viguno/hpo-{v_hpo}+{v_viguno}/spec.yaml",
     wildcard_constraints:
@@ -61,21 +57,4 @@ rule subset_worker_pheno_dev:  # -- create development subset
         cp -a {input.phenotype_to_genes} {output.phenotype_to_genes}
         cp -a {input.bin} {output.bin}
         cp -a {input.spec_yaml} {output.spec_yaml}
-
-        viguno simulate \
-            --ic-base gene \
-            --similarity resnik \
-            --combiner fun-sim-avg \
-            --path-hpo-dir $(dirname {input.obo}) \
-            --path-out-rocksdb $(dirname {output.rocksdb_identity}) \
-            --min-terms 1 \
-            $(if [[ "{RUNS_IN_CI}" == "True" ]]; then \
-                echo --max-terms 1; \
-                echo --num-simulations 10; \
-                echo --only-gene ARID1B; \
-            else \
-                echo --max-terms 10; \
-                echo --num-simulations 100; \
-            fi) \
-            --seed 42
         """