Merge pull request #69 from gregdenay/master

MIDORI

ressources/create_MIDORI_blastdb.sh

@@ -0,0 +1,29 @@
+# Get MIDORI Fasta and reformat header
+wget -S -P ./source/ https://www.reference-midori.info/forceDownload.php?fName=download/Databases/GenBank259_2023-12-17/BLAST/uniq/fasta/MIDORI2_UNIQ_NUC_GB259_lrRNA_BLAST.fasta.zip \
+    && gunzip -c ./source/MIDORI2_UNIQ_NUC_GB259_lrRNA_BLAST.fasta.zip > ./source/MIDORI2_UNIQ_NUC_GB259_lrRNA_BLAST.fasta \
+    && cut -d '#' -f1 ./source/MIDORI2_UNIQ_NUC_GB259_lrRNA_BLAST.fasta \
+        | tr -d '<' \
+        | sed 's/^>/@/' \
+        | tr -d '>' \
+        | tr '@' '>' \
+        | cut -d ',' -f1,2 \
+        | tr ',' '_' \
+        > MIDORI2_UNIQ_NUC_GB259_lrRNA_BLAST.fasta
+
+# taxdb
+wget -S -P ./source/ https://ftp.ncbi.nlm.nih.gov/blast/db/taxdb.tar.gz \
+	&& tar -xzvf ./source/taxdb.tar.gz 
+
+# taxdump
+wget -S -P ./source/ https://ftp.ncbi.nlm.nih.gov/pub/taxonomy/new_taxdump/new_taxdump.tar.gz \
+    && tar -xzvf ./source/new_taxdump.tar.gz
+
+# taxid file
+# Get taxid from fasta headers
+paste \
+    <(cat ./source/MIDORI2_UNIQ_NUC_GB259_lrRNA_BLAST.fasta | grep '^>' | cut -d '#' -f1 | tr -d '<' | tr -d '>' | cut -d ',' -f1,2 | tr ',' '_') \
+    <(cat ./source/MIDORI2_UNIQ_NUC_GB259_lrRNA_BLAST.fasta | grep '^>' | rev | cut -d '_' -f1 | rev) \
+    > ids2taxid
+
+# Make db
+makeblastdb -in MIDORI2_UNIQ_NUC_GB259_lrRNA_BLAST.fasta -parse_seqids -blastdb_version 5 -taxid_map ids2taxid -dbtype nucl

workflow/paramspace

@@ -20,6 +20,18 @@ workdir: config["workdir"]
 paramspace = Paramspace(pd.read_csv(config['paramspace'], sep="\t"))
 
 
+# Snakemake 8 compatibility ----------------------------------------------------
+
+
+def get_conda_prefix(wildcards):
+    try:
+        # snakemake < 8.0
+        return workflow.conda_prefix
+    except:
+        # snakemake > 8
+        return workflow.deployment_settings.conda_prefix
+
+
 # Input rule ------------------------------------------------------------------
 
 
@@ -68,7 +80,7 @@ rule run_foodme_benchmark:
         workdir=f"foodme_runs/{paramspace.wildcard_pattern}",
         snakefile=os.path.join(workflow.basedir, "benchmark"),
         cores=workflow.cores,
-        conda_prefix=workflow.conda_prefix,
+        conda_prefix=get_conda_prefix,
         force_rerun="--forceall" if config["force_rerun"] else ""
     log:
         f"logs/{paramspace.wildcard_pattern}/snakemake.log"