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Merge pull request #245 from Irallia/TEST/BENCHMARK/dataset_compariso…
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…n/cleanup_plot

[BENCHMARK] dataset comparison: cleanup plots
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@Irallia
Irallia authored Nov 21, 2022
2 parents 70a8354 + 843ff66 commit 501e064
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Showing 6 changed files with 3 additions and 78 deletions.
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27 changes: 1 addition & 26 deletions test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.DEL.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -58,18 +58,6 @@ rule cat_truvari_results_DEL:
min_qual = min_qual_iGenVar),
S2 = expand("results/caller_comparison_iGenVar_only/eval/S2/DEL.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
S1L1 = expand("results/caller_comparison_iGenVar_only/eval/S1L1/DEL.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
S2L1 = expand("results/caller_comparison_iGenVar_only/eval/S2L1/DEL.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
S1L2 = expand("results/caller_comparison_iGenVar_only/eval/S1L2/DEL.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
S2L2 = expand("results/caller_comparison_iGenVar_only/eval/S2L2/DEL.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
S1L3 = expand("results/caller_comparison_iGenVar_only/eval/S1L3/DEL.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
S2L3 = expand("results/caller_comparison_iGenVar_only/eval/S2L3/DEL.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
L1 = expand("results/caller_comparison_iGenVar_only/eval/L1/DEL.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
L2 = expand("results/caller_comparison_iGenVar_only/eval/L2/DEL.min_qual_{min_qual}/pr_rec.txt",
Expand All @@ -79,12 +67,6 @@ rule cat_truvari_results_DEL:
output:
S1 = temp("results/caller_comparison_iGenVar_only/eval/S1.DEL_results.txt"),
S2 = temp("results/caller_comparison_iGenVar_only/eval/S2.DEL_results.txt"),
S1L1 = temp("results/caller_comparison_iGenVar_only/eval/S1L1.DEL_results.txt"),
S2L1 = temp("results/caller_comparison_iGenVar_only/eval/S2L1.DEL_results.txt"),
S1L2 = temp("results/caller_comparison_iGenVar_only/eval/S1L2.DEL_results.txt"),
S2L2 = temp("results/caller_comparison_iGenVar_only/eval/S2L2.DEL_results.txt"),
S1L3 = temp("results/caller_comparison_iGenVar_only/eval/S1L3.DEL_results.txt"),
S2L3 = temp("results/caller_comparison_iGenVar_only/eval/S2L3.DEL_results.txt"),
L1 = temp("results/caller_comparison_iGenVar_only/eval/L1.DEL_results.txt"),
L2 = temp("results/caller_comparison_iGenVar_only/eval/L2.DEL_results.txt"),
L3 = temp("results/caller_comparison_iGenVar_only/eval/L3.DEL_results.txt"),
Expand All @@ -93,17 +75,10 @@ rule cat_truvari_results_DEL:
run:
shell("cat {input.S1} > {output.S1}")
shell("cat {input.S2} > {output.S2}")
shell("cat {input.S1L1} > {output.S1L1}")
shell("cat {input.S2L1} > {output.S2L1}")
shell("cat {input.S1L2} > {output.S1L2}")
shell("cat {input.S2L2} > {output.S2L2}")
shell("cat {input.S1L3} > {output.S1L3}")
shell("cat {input.S2L3} > {output.S2L3}")
shell("cat {input.L1} > {output.L1}")
shell("cat {input.L2} > {output.L2}")
shell("cat {input.L3} > {output.L3}")
shell("""
cat {output.S1} {output.S2} {output.S1L1} {output.S2L1} \
{output.S1L2} {output.S2L2} {output.S1L3} {output.S2L3} \
cat {output.S1} {output.S2} \
{output.L1} {output.L2} {output.L3} > {output.all}
""")
27 changes: 1 addition & 26 deletions test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.INS.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -58,18 +58,6 @@ rule cat_truvari_results_INS:
min_qual = min_qual_iGenVar),
S2 = expand("results/caller_comparison_iGenVar_only/eval/S2/INS.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
S1L1 = expand("results/caller_comparison_iGenVar_only/eval/S1L1/INS.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
S2L1 = expand("results/caller_comparison_iGenVar_only/eval/S2L1/INS.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
S1L2 = expand("results/caller_comparison_iGenVar_only/eval/S1L2/INS.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
S2L2 = expand("results/caller_comparison_iGenVar_only/eval/S2L2/INS.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
S1L3 = expand("results/caller_comparison_iGenVar_only/eval/S1L3/INS.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
S2L3 = expand("results/caller_comparison_iGenVar_only/eval/S2L3/INS.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
L1 = expand("results/caller_comparison_iGenVar_only/eval/L1/INS.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
L2 = expand("results/caller_comparison_iGenVar_only/eval/L2/INS.min_qual_{min_qual}/pr_rec.txt",
Expand All @@ -79,12 +67,6 @@ rule cat_truvari_results_INS:
output:
S1 = temp("results/caller_comparison_iGenVar_only/eval/S1.INS_results.txt"),
S2 = temp("results/caller_comparison_iGenVar_only/eval/S2.INS_results.txt"),
S1L1 = temp("results/caller_comparison_iGenVar_only/eval/S1L1.INS_results.txt"),
S2L1 = temp("results/caller_comparison_iGenVar_only/eval/S2L1.INS_results.txt"),
S1L2 = temp("results/caller_comparison_iGenVar_only/eval/S1L2.INS_results.txt"),
S2L2 = temp("results/caller_comparison_iGenVar_only/eval/S2L2.INS_results.txt"),
S1L3 = temp("results/caller_comparison_iGenVar_only/eval/S1L3.INS_results.txt"),
S2L3 = temp("results/caller_comparison_iGenVar_only/eval/S2L3.INS_results.txt"),
L1 = temp("results/caller_comparison_iGenVar_only/eval/L1.INS_results.txt"),
L2 = temp("results/caller_comparison_iGenVar_only/eval/L2.INS_results.txt"),
L3 = temp("results/caller_comparison_iGenVar_only/eval/L3.INS_results.txt"),
Expand All @@ -93,17 +75,10 @@ rule cat_truvari_results_INS:
run:
shell("cat {input.S1} > {output.S1}")
shell("cat {input.S2} > {output.S2}")
shell("cat {input.S1L1} > {output.S1L1}")
shell("cat {input.S2L1} > {output.S2L1}")
shell("cat {input.S1L2} > {output.S1L2}")
shell("cat {input.S2L2} > {output.S2L2}")
shell("cat {input.S1L3} > {output.S1L3}")
shell("cat {input.S2L3} > {output.S2L3}")
shell("cat {input.L1} > {output.L1}")
shell("cat {input.L2} > {output.L2}")
shell("cat {input.L3} > {output.L3}")
shell("""
cat {output.S1} {output.S2} {output.S1L1} {output.S2L1} \
{output.S1L2} {output.S2L2} {output.S1L3} {output.S2L3} \
cat {output.S1} {output.S2} \
{output.L1} {output.L2} {output.L3} > {output.all}
""")
27 changes: 1 addition & 26 deletions test/benchmark/caller_comparison_iGenVar_only/workflow/rules/eval.no_DUP_and_INV.smk
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Original file line number Diff line number Diff line change
Expand Up @@ -85,18 +85,6 @@ rule no_DUP_and_INV_cat_truvari_results_all:
min_qual = min_qual_iGenVar),
S2 = expand("results/caller_comparison_iGenVar_only/eval/S2/no_DUP_and_INV.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
S1L1 = expand("results/caller_comparison_iGenVar_only/eval/S1L1/no_DUP_and_INV.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
S2L1 = expand("results/caller_comparison_iGenVar_only/eval/S2L1/no_DUP_and_INV.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
S1L2 = expand("results/caller_comparison_iGenVar_only/eval/S1L2/no_DUP_and_INV.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
S2L2 = expand("results/caller_comparison_iGenVar_only/eval/S2L2/no_DUP_and_INV.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
S1L3 = expand("results/caller_comparison_iGenVar_only/eval/S1L3/no_DUP_and_INV.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
S2L3 = expand("results/caller_comparison_iGenVar_only/eval/S2L3/no_DUP_and_INV.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
L1 = expand("results/caller_comparison_iGenVar_only/eval/L1/no_DUP_and_INV.min_qual_{min_qual}/pr_rec.txt",
min_qual = min_qual_iGenVar),
L2 = expand("results/caller_comparison_iGenVar_only/eval/L2/no_DUP_and_INV.min_qual_{min_qual}/pr_rec.txt",
Expand All @@ -106,12 +94,6 @@ rule no_DUP_and_INV_cat_truvari_results_all:
output:
S1 = temp("results/caller_comparison_iGenVar_only/eval/S1.no_DUP_and_INV_results.txt"),
S2 = temp("results/caller_comparison_iGenVar_only/eval/S2.no_DUP_and_INV_results.txt"),
S1L1 = temp("results/caller_comparison_iGenVar_only/eval/S1L1.no_DUP_and_INV_results.txt"),
S2L1 = temp("results/caller_comparison_iGenVar_only/eval/S2L1.no_DUP_and_INV_results.txt"),
S1L2 = temp("results/caller_comparison_iGenVar_only/eval/S1L2.no_DUP_and_INV_results.txt"),
S2L2 = temp("results/caller_comparison_iGenVar_only/eval/S2L2.no_DUP_and_INV_results.txt"),
S1L3 = temp("results/caller_comparison_iGenVar_only/eval/S1L3.no_DUP_and_INV_results.txt"),
S2L3 = temp("results/caller_comparison_iGenVar_only/eval/S2L3.no_DUP_and_INV_results.txt"),
L1 = temp("results/caller_comparison_iGenVar_only/eval/L1.no_DUP_and_INV_results.txt"),
L2 = temp("results/caller_comparison_iGenVar_only/eval/L2.no_DUP_and_INV_results.txt"),
L3 = temp("results/caller_comparison_iGenVar_only/eval/L3.no_DUP_and_INV_results.txt"),
Expand All @@ -120,17 +102,10 @@ rule no_DUP_and_INV_cat_truvari_results_all:
run:
shell("cat {input.S1} > {output.S1}")
shell("cat {input.S2} > {output.S2}")
shell("cat {input.S1L1} > {output.S1L1}")
shell("cat {input.S2L1} > {output.S2L1}")
shell("cat {input.S1L2} > {output.S1L2}")
shell("cat {input.S2L2} > {output.S2L2}")
shell("cat {input.S1L3} > {output.S1L3}")
shell("cat {input.S2L3} > {output.S2L3}")
shell("cat {input.L1} > {output.L1}")
shell("cat {input.L2} > {output.L2}")
shell("cat {input.L3} > {output.L3}")
shell("""
cat {output.S1} {output.S2} {output.S1L1} {output.S2L1} \
{output.S1L2} {output.S2L2} {output.S1L3} {output.S2L3} \
cat {output.S1} {output.S2} \
{output.L1} {output.L2} {output.L3} > {output.all}
""")

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