BLAST query against remote NCBI DBs

BLAST the input query against remote NCBI DBs (one sequence at a time - to respect rate limits)

RemoteBLAST(
  ptr,
  database,
  query_input,
  input_type,
  outFile = NULL,
  outFormat = NULL,
  return_values = TRUE,
  max_poll_seconds = 360L,
  poll_interval_ms = 4000L,
  verbose = TRUE
)

Arguments

ptr

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

database

(string) Name of the remote NCBI DB - Check note for reference and supported values.

query_input

(Rcpp::List) (Named) List of input queries (Sequences, Files, Folders - type is determined by input_type parameter)

input_type

(QuickBLAST::EInputType) Input type (Check GetQuickBLASTEnums())

outFile

(string) Output file name (Optional)

outFormat

(string) Format of Output File (Required for outFile) (Default: 'parquet')

return_values

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

max_poll_seconds

(int) Max seconds to wait for RemoteBLAST (Default: 360) (Optional)

poll_interval_ms

(int) Milliseconds wait-time between polling RemoteBLAST service (Default(4s): 4000) (Optional)

verbose

(bool) Verbosity (Default: TRUE).

Value

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

Note

Check BLAST Guide (https://blast.ncbi.nlm.nih.gov/BLAST_guide.pdf) and NCBI BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi) (Program -> Choose DB/Search set) for database names.

See also

GetInstanceID(), GetQuickBLASTInstance(), 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
)
QuickBLAST::RemoteBLAST(
  blastp_inst,
  query_input="MQILLVEDDNTLFQELKKELEQWDFN
  VAGIEDFGKVMDTFESFNPEIVILDVQLPKYDGFYWCRK
  MREVSNVPILFLSSRDNPMDQVMSMELGADDYMQKPFYT
  NVLIAKLQAIYRRVYEFTAEEKRTLTWQDAVVDLSKDSI
  QKGDDTIFLSKTEMIILEILITKKNQIVSRDTIITALWD
  DEAFVSDNTLTVNVNRLRKKLSEISMDSAIETKVGKGYMAHE",
  database= "pdb",
  input_type=1,
  return_values=T
)
} # }