Make on-disk BLAST DB from a FASTA file

Calls makeblastdb to create a BLAST DB of a FASTA file

MakeBLASTDB(ptr, input_file, database_name, parse_seqids = FALSE)

Arguments

ptr

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

input_file

(string) Path to FASTA file.

database_name

(string) Name of the output DB.

parse_seqids

(bool) TRUE - Checks FASTA headers for malformations (Default: FALSE)

Value

(bool) DB name on success, FALSE - Otherwise.

Note

Faitful re-implementation of makeblastdb seemed pointless, hence the system.call() to a the program.

See also

GetInstanceID(), GetQuickBLASTInstance(), BLAST2DBs(), isBLASTDB()

Examples

if (FALSE) { # \dontrun{
blastp_inst <- QuickBLAST::CreateQuickBLASTInstance(
  seq_type = 1,
  strand = 0,
  program = "blastp",
  save_sequences = F,
  save_hsp_sequences = F
)
QuickBLAST::MakeBLASTDB(
  blastp_inst,
  system.file(
    "extdata",
    "protein_query.fasta",
    package = "QuickBLAST",
    mustWork = T
  ),
  "protein_query.db"
)
QuickBLAST::MakeBLASTDB(
  blastp_inst,
  system.file(
    "extdata",
    "protein_subject.fasta",
    package = "QuickBLAST",
    mustWork = T
  ),
  "protein_subject.db"
)
QuickBLAST::BLAST2DBs(
  ptr=blastp_inst,
  query="protein_query.db",
  subject="protein_subject.db",
  num_threads=24,
  out_file="test.db.arrow",
  return_values = T
)
} # }