run_pureseqtm_proteome: Run PureseqTM on a proteome

In pureseqtmr: Predict Transmembrane Protein Topology

Run PureseqTM on a proteome

Description

Run PureseqTM on a proteome

Usage

run_pureseqtm_proteome(
  fasta_filename,
  folder_name = get_default_pureseqtm_folder(),
  topology_filename = tempfile(fileext = ".top")
)

Arguments

fasta_filename	path to a FASTA file
folder_name	superfolder of PureseqTM. The superfolder's name is /home/[user_name]/.local/share by default, as can be obtained by get_default_pureseqtm_folder
topology_filename	name of the file to save a protein's topology to

Value

the topology of the proteome, using the same output as PureseqTM. Use predict_topology to get the topology as a tibble

Author(s)

Richèl J.C. Bilderbeek

See Also

• Use predict_topology to predict the topology of a proteome

• Use create_pureseqtm_files to only create the PureseqTM output files

Examples

if (is_pureseqtm_installed()) {
  fasta_filename <- get_example_filename("1bhaA.fasta")
  run_pureseqtm_proteome(fasta_filename)
}

pureseqtmr documentation built on April 6, 2023, 5:20 p.m.