From 43de483788515ff2665ebef9d6920bde82239f1d Mon Sep 17 00:00:00 2001 From: Luiz Irber Date: Sat, 30 Sep 2023 10:16:44 -0700 Subject: [PATCH] prepare genbank DBs --- experiments/Snakefile | 18 +++++++++++++++++- 1 file changed, 17 insertions(+), 1 deletion(-) diff --git a/experiments/Snakefile b/experiments/Snakefile index 11ad8fe..39248f1 100644 --- a/experiments/Snakefile +++ b/experiments/Snakefile @@ -2,7 +2,8 @@ EXEC="cargo run -p mastiff-index --release -- " rule all: # input: "outputs/rs207" - input: "outputs/rs207-2k" +# input: "outputs/rs207-2k" + input: expand("outputs/genbank-{domain}", domain=["archaea", "bacteria", "fungi", "protozoa", "viral"]) rule rs207_1k: output: directory("outputs/rs207-1k") @@ -148,6 +149,21 @@ rule catalog_metagenomes: sig_path = path / "sigs" / f"{sra_id}.sig" if sig_path.exists(): out.write(f"{sig_path}\n") + out.flush() + +####################################################################### + +rule genbank: + output: directory("outputs/genbank-{domain}") + input: "/data/wort/databases/genbank-2022.03-{domain}-k21.zip" + + shell: """ + {EXEC} index -k 21 -s 1000 \ + --output {output} \ + {input} + """ + +####################################################################### """ {EXEC} index -k 21 -s 1000 --output /scratch/analysis/rocksdb_metagenomes catalog_metagenomes