run_tmhmm: Run TMHMM on a FASTA file with one or more proteins.

In richelbilderbeek/tmhmm: Interface to TMHMM

Run TMHMM on a FASTA file with one or more proteins.

Description

The function run_tmhmm_on_one_protein_fasta_file is the function that actually calls TMHMM, on a per-protein basis.

Usage

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

Arguments

fasta_filename	path to a FASTA file
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

Value

the topology as text, in a similar form as a FASTA file, for example c(">Protein A", "iiiimmmmmoooo"). Use predict_topology to get the same result in the form of a tibble

Author(s)

Richèl J.C. Bilderbeek

See Also

Use mock_run_tmhmm to mock this function

Examples

if (is_tmhmm_installed()) {
  fasta_filename <- system.file("extdata", "tmhmm.fasta", package = "tmhmm")
  topology_text <- run_tmhmm(fasta_filename)
  cat(topology_text, sep = "\n")
}

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