Check BLAST DB Files

Check whether a path/name corresponds to a BLAST DB (heuristic). Check if all the files of a BLAST DB exist (.psq .pog .pin .phr .pos .pto .pot .pdb .ptf .pjs). This checks the directory for filenames that start with the provided basename and have extensions commonly produced by makeblastdb:

• protein: .phr .pin .psq

• nucleotide: .nhr .nin .nsq It returns a list with a boolean is_db, a guessed type ("Protein"/"Nucleotide"/"Mixed"/"Unknown"), a character vector of matching files, and the dir and name used.

isBLASTDB(ptr, input_db)

Arguments

ptr

(Rcpp::XPtr<QuickBLAST>) or (unsigned int) Pointer/ID of QuickBLAST instance

input_db

character(1) path to db (path + name) or a bare name (current directory assumed)

Value

list with keys: is_db (logical), type (string), files (character vector), dir (string), name (string), message (string)

See also

GetInstanceID(), GetQuickBLASTInstance(), MakeBLASTDB(), BLAST2DBs()

Examples

if (FALSE) { # \dontrun{
QuickBLAST::MakeBLASTDB(
  blastp_inst,
  system.file(
    "extdata",
    "protein_query.fasta",
    package = "QuickBLAST",
    mustWork = T
  ),
  "protein_query.db"
)
QuickBLAST::isBLASTDB(
  tools::file_path_sans_ext(
    system.file(
      "extdata",
      "protein_query.db.pin",
      package = "QuickBLAST",
      mustWork = T
    )
  )
)
} # }