BLAST 2 Files

BLAST 2 FASTA files containing nucleotide or protein sequences with a QuickBLAST instance.

BLAST2Files(
  ptr,
  query,
  subject,
  out_file = NULL,
  out_format = NULL,
  num_threads = 0L,
  return_values = TRUE,
  min_batch_size = 0L,
  verbose = TRUE
)

Arguments

ptr

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

query

(string) Query file

subject

(string) Subject file

out_file

(string) Ouput file (Optional)

out_format

(string) Ouput Format. 'ipc'/'csv'/'parquet' (Optional) (Default: 'parquet').

num_threads

(unsigned int) Number of threads. (Optional)

return_values

(bool) Return BLAST Hits as Rcpp::List (Default: TRUE) (Optional)

min_batch_size

(unsigned int) Minimum batch size - Size of file write buffer (Optional).

verbose

(bool) Verbosity (Default: TRUE).

Value

(SEXP) Rcpp::List - if return_values == TRUE, out_file - Otherwise.

Note

Only FASTA files are supported by this function, use BLAST2DBs() if inputs are BLAST DBs.

See also

GetInstanceID(), GetQuickBLASTInstance(), BLAST2Files(), BLAST2DBs(), BLAST2Seqs(), BLAST2Folders(), BLAST1Folder(), RemoteBLAST()

Examples

if (FALSE) { # \dontrun{
blastp_inst <- QuickBLAST::CreateQuickBLASTInstance(
  seq_type = 1,
  strand = 0,
  program = "blastp",
  save_sequences = F,
  save_hsp_sequences = F
)
QuickBLAST::BLAST2Files(
  ptr = blastp_inst,
  query = system.file(
    "extdata",
    "protein_query.fasta",
    package = "QuickBLAST",
    mustWork = T
  ),
  subject = system.file(
    "extdata",
    "protein_subject.fasta",
    package = "QuickBLAST",
    mustWork = T
  ),
  out_file = "test.arrow",
  out_format = "parquet",
  return_values = F,
  min_batch_size = 1024
)
QuickBLAST::BLAST2Files(
  ptr = blastp_inst,
  query = system.file(
    "extdata",
    "protein_query.fasta",
    package = "QuickBLAST",
    mustWork = T
  ),
  subject = system.file(
    "extdata",
    "protein_subject.fasta",
    package = "QuickBLAST",
    mustWork = T
  ),
  out_file = "test.arrow",
  return_values = T,
  min_batch_size = 0,
  seq_limit = 0
)
} # }