BLAST Files within a Folder

BLAST FASTA files containing nucleotide or protein sequences, within a folder with a QuickBLAST instance. The files from the folder are selected with the extension parameter and BLAST'd against each other.

BLAST1Folder(
  ptr,
  input_folder,
  extension,
  out_folder,
  out_format = NULL,
  num_threads = 0L,
  reciprocal_hits = FALSE,
  min_batch_size = 0L,
  verbose = TRUE
)

Arguments

ptr

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

input_folder

(string) Input folder

extension

(string) Extension of files in folder.

out_folder

(string) Ouput Folder (Required).

out_format

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

num_threads

(unsigned int) Number of threads. (Optional)

reciprocal_hits

(bool) Perform Bi-directional (Reciprocal => query <-> subject) BLAST? (Default: FALSE) (Optional)

min_batch_size

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

verbose

(bool) Verbosity (Defulat: TRUE).

Value

(bool) TRUE - on success, FALSE - Otherwise. (Results are not returned as R Lists to reduce overhead)

Note

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

See also

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

Examples

blastp_inst <- QuickBLAST::CreateQuickBLASTInstance(
  seq_type = 1,
  strand = 0,
  program = "blastp",
  save_sequences = FALSE,
  save_hsp_sequences = FALSE
)
#> Using blastp Defaults...
QuickBLAST::BLAST1Folder(
  ptr = blastp_inst,
  input_folder = system.file(
    "extdata",
    package = "QuickBLAST",
    mustWork = TRUE
  ),
  extension = "fasta",
  out_folder = tempdir(),
  out_format = "parquet",
  reciprocal_hits = TRUE,
  min_batch_size = 1024
)
#> [1] TRUE