run_tmhmm_to_file: Creates a FASTA-like file, that has the locations of the...

In richelbilderbeek/tmhmm: Interface to TMHMM

Creates a FASTA-like file, that has the locations of the amino acids.

Description

Creates a FASTA-like file, that has the locations of the amino acids.

Usage

run_tmhmm_to_file(
  fasta_filename,
  tmhmm_filename,
  one_protein_fasta_filename = tempfile(fileext = ".fasta"),
  folder_name = get_default_tmhmm_folder()
)

Arguments

fasta_filename	path to a FASTA file
tmhmm_filename	filename to write the TMHMM results to
one_protein_fasta_filename	name of a FASTA file, that contains one name and one sequence
folder_name	superfolder of TMHMM. The superfolder's name is /home/[user_name]/.local/share by default, as can be obtained by get_default_tmhmm_folder

Examples

if (is_tmhmm_installed()) {

  # Write results to a temporary file
  tmhmm_filename <- tempfile()
  run_tmhmm_to_file(
    fasta_filename = system.file(
      "extdata", "tmhmm.fasta", package = "tmhmm"
    ),
    tmhmm_filename = tmhmm_filename
  )

  # Result is written to 'tmhmm_filename', cleaning up
  file.remove(tmhmm_filename)
}

richelbilderbeek/tmhmm documentation built on Sept. 3, 2022, 5:14 p.m.