predict_topology_from_sequence: Run TMHMM directy on a protein sequence

In richelbilderbeek/tmhmm: Interface to TMHMM

Run TMHMM directy on a protein sequence

Description

Run TMHMM directy on a protein sequence

Usage

predict_topology_from_sequence(
  protein_sequence,
  folder_name = get_default_tmhmm_folder(),
  temp_fasta_filename = tempfile(fileext = ".fasta"),
  temp_topology_filename = tempfile(fileext = ".topo")
)

Arguments

protein_sequence	a protein 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
temp_fasta_filename	filename to temporarily save the protein names and sequences. This file will be deleted when this function completed successfully
temp_topology_filename	filename to temporarily save the topology. This file will be deleted when this function completed successfully

Value

a topology sequence, for example "iiiimmmmmoooo"

Author(s)

Richèl J.C. Bilderbeek

See Also

Use mock_predict_topology_from_sequence to do a mock prediction

Examples

if (is_tmhmm_installed()) {
  protein_sequence <- paste0(
    "QEKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLM",
    "SLAIADMLLGFLVMPVSMLTILYGYRWP"
  )
  predict_topology_from_sequence(protein_sequence)
}

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