Make BLAST Database — make_blast_db • BLASTr

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 = "silent",
  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")

Value

The result of the makeblastdb command.

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"
)
} # }