From ce2e92a5e043531c190e1827d9b9f1352978c9aa Mon Sep 17 00:00:00 2001 From: christinehc Date: Fri, 1 Apr 2022 13:02:02 -0700 Subject: [PATCH 1/2] Clean up unnecessary comment(s) --- snekmer/rules/model.smk | 1 - 1 file changed, 1 deletion(-) diff --git a/snekmer/rules/model.smk b/snekmer/rules/model.smk index 469eb6d..d41dd25 100644 --- a/snekmer/rules/model.smk +++ b/snekmer/rules/model.smk @@ -375,7 +375,6 @@ rule model: ) # collate ROC-AUC results - # collate PR-AUC results results["family"] += [family] * cv results["alphabet_name"] += [alphabet_name.lower()] * cv results["k"] += [config["k"]] * cv From 649fecb4e942a7953ad18a9f8bddb47e5bdc7f06 Mon Sep 17 00:00:00 2001 From: christinehc Date: Tue, 5 Apr 2022 08:31:01 -1000 Subject: [PATCH 2/2] Correct variable name for cluster filename wildcards. Fixes #46 The variable name `fa_map` was erroneously carried from a previous iteration of the code; the variable name was changed to `FA_MAP` but references to `fa_map` had not all been replaced in the cluster workflow. The incorrect references have been corrected. --- snekmer/rules/cluster.smk | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/snekmer/rules/cluster.smk b/snekmer/rules/cluster.smk index 87f703d..01d4a8a 100644 --- a/snekmer/rules/cluster.smk +++ b/snekmer/rules/cluster.smk @@ -101,7 +101,7 @@ use rule unzip from process_input with: # read and process parameters from config use rule preprocess from process_input with: input: - fasta=lambda wildcards: join("input", f"{wildcards.nb}.{fa_map[wildcards.nb]}"), + fasta=lambda wildcards: join("input", f"{wildcards.nb}.{FA_MAP[wildcards.nb]}"), output: data=join(out_dir, "processed", "full", "{nb}.json"), desc=join(out_dir, "processed", "full", "{nb}_description.csv"), @@ -124,7 +124,7 @@ use rule vectorize_full from kmerize with: input: kmers=join(out_dir, "labels", "full", "{nb}.txt"), params=join(out_dir, "processed", "{nb}.json"), - fasta=lambda wildcards: join("input", f"{wildcards.nb}.{fa_map[wildcards.nb]}"), + fasta=lambda wildcards: join("input", f"{wildcards.nb}.{FA_MAP[wildcards.nb]}"), log: join(out_dir, "features", "log", "{nb}.log"), output: