Create new QuickBLAST instance with seq_type, strand, program and BLAST options.

Create a new QuickBLAST C++ object with seq_type, strand, program and BLAST options, which can be used in QuickBLAST::BLAST2Files() and QuickBLAST::BLAST2Seqs()

CreateQuickBLASTInstance(
  seq_type,
  strand,
  program,
  options = NULL,
  save_sequences = FALSE,
  save_hsp_sequences = FALSE
)

Arguments

seq_type

(int) 0 - (eNucleotide) (OR) 1 - (eProtein)

strand

(int) 0 - (ePlus) (OR) 1 - (eMinus)

program

(string) Name of the BLAST program

options

(string (or) Named List) List of BLAST options - check QuickBLAST::GetAvailableBLASTOptions(). String should be of the format "-option1 value1 -option2 value2". If empty, default values (per program) are used.

save_sequences

(bool) Save Full Sequences to output?. (Default: FALSE)

save_hsp_sequences

(bool) Save HSP Sequences to output?. (Default: FALSE)

Value

(Rcpp::XPtr<QuickBLAST>) Pointer to a QuickBLAST Instance (Cannot be used in R)

Note

Set save_sequences AND/OR save_hsp_sequences when using Genomes

See also

GetAvailableBLASTOptions(), GetQuickBLASTEnums(), BLAST2Files(), 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
)
} # }