predict_topologies_from_sequences: 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_topologies_from_sequences(
  protein_sequences,
  folder_name = get_default_tmhmm_folder(),
  temp_fasta_filename = tempfile(fileext = ".fasta"),
  temp_topology_filename = tempfile(fileext = ".topo")
)

Arguments

protein_sequences	one or more protein sequences
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

one or more topology sequences, for example c("iiiimmmmooooo", "iiiii")

Author(s)

Richèl J.C. Bilderbeek

See Also

use mock_predict_topologies_from_sequences to mock the prediction of protein sequences, as can be useful in testing

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.