run_tmhmm_on_one_protein_fasta_file: Run TMHMM on a FASTA file with one protein

In richelbilderbeek/tmhmm: Interface to TMHMM

Run TMHMM on a FASTA file with one protein

Description

This is the function that actually calls TMHMM. The usage of TMHMM us split up per protein, as R cannot handle communication via stdin that is too long, hence, bigger FASTA files get truncated, and a topology of less proteins is returned.

Usage

run_tmhmm_on_one_protein_fasta_file(
  one_protein_fasta_filename,
  folder_name = get_default_tmhmm_folder()
)

Arguments

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

Details

Use run_tmhmm to call TMHMM with a FASTA file with multiple lines.

Value

text similar to a FASTA file, yet with the predicted topology instead of the protein sequence

Author(s)

Richèl J.C. Bilderbeek

Examples

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

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