Execute all2all QuickBLAST

Source: R/QuickBLAST.R

Executes All-to-All QuickBLAST between two lists of organisms/genes/clusters. Output BLAST files are bi-directional and are stored in the filename filename1.filename2.all2all under output_dir. (All-to-All is simply Many-to-Many association)

all2all(
  first_list,
  second_list,
  blast_fun,
  seq_type,
  strand,
  blast_program,
  file_ext = ".fa",
  input_prefix_path = NULL,
  output_dir = "./",
  ...
)

Arguments

first_list

Vector of FASTA Filenames or Strings

second_list

Vector of FASTA Filenames or Strings

blast_fun

One of QuickBLAST::BLAST2Seqs, QuickBLAST::BLAST2Files, QuickBLAST::BLAST2Folders, QuickBLAST::BLAST2DBs

seq_type

(int) Sequence Type. Check QuickBLAST::GetQuickBLASTEnums()$ESeqType for available enums.

strand

(int) Strand. Check QuickBLAST::GetQuickBLASTEnums()$EStrand for available enums.

blast_program

Give the name of the BLAST program to use (if in $PATH) or give the absolute path to the BLAST program.

file_ext

File extension of input files. eg- ".cds" or ".fa", Unused if input_type is GetQuickBLASTEnums()$EInputType$eSequencesString

input_prefix_path

If input lists/vectors are filenames, then provide input folder to prefix path

output_dir

Path to BLAST output

...

Extended options passed to internal functions, including:

  • blast_options: BLAST Options to use - QuickBLAST::GetAvailableBLASTOptions()

  • save_sequences: (bool) Save full sequences to result?

  • save_hsp_sequences: (bool) Save HSP sequences to result?

  • return_values: (bool) Return values back to R?

  • min_batch_size: Minimum batch size. (Default: 256)

  • n_threads: Number of threads. (Default: 8)

  • out_format: Output format. ipc/csv/parquet (Default: "parquet")

  • extension: File extension. (Only for QuickBLAST::BLAST2Folders())

  • reciprocal_hits: (bool) Reciprocal (Bi-directional) Hits?

  • verbose: (bool) Print DEBUG Messages?

Examples

if (FALSE) { # \dontrun{
QuickBLAST::all2all(
  first_list=fs::path_package("QuickBLAST", "extdata", "protein_query.fasta"),
  second_list=fs::path_package("QuickBLAST", "extdata", "protein_subject.fasta"), 
  blast_fun=QuickBLAST::BLAST2Files,
  seq_type = 0, 
  strand=0,
  output_dir = "./",
  n_threads = 8,
  blast_program = "tblastx",
  save_sequences=FALSE,
  save_hsp_sequences=FALSE,
  return_values=TRUE,
  min_batch_size=256,
  out_format="parquet",
  blast_options="",
  verbose = TRUE
 )
} # }