Create a BLAST database from a FASTA file.
Usage
make_blast_db(
fasta_path,
db_path,
db_type = "nucl",
taxid_map = NULL,
parse_seqids = TRUE,
verbose = FALSE,
env_name = "blastr-blast-env"
)Arguments
- fasta_path
Path to the input FASTA file.
- db_path
Path to the output BLAST database.
- db_type
Type of database to create, either "nucl" or "prot".
- taxid_map
Optional path to a file mapping sequence IDs to taxonomy IDs.
- parse_seqids
Whether to parse sequence IDs.
- verbose
Should condathis::run() internal command be shown?
- env_name
The name of the conda environment with the parameter (i.e. "blastr-blast-env")
Examples
if (FALSE) { # \dontrun{
make_blast_db(
fasta_path = fs::path_package(
"BLASTr", "extdata", "minimal_db_blast",
ext = "fasta"
),
db_path = fs::path_temp("minimal_db_blast"),
db_type = "nucl"
)
} # }