mock_run_tmhmm: Mock run_tmhmm

In richelbilderbeek/tmhmm: Interface to TMHMM

Mock run_tmhmm

Description

Mock run_tmhmm

Usage

mock_run_tmhmm(
  fasta_filename,
  one_protein_fasta_filename = "ignored",
  folder_name = "ignored"
)

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

Examples

fasta_filename <- system.file("extdata", "tmhmm.fasta", package = "tmhmm")
topology_text <- mock_run_tmhmm(fasta_filename)
cat(topology_text, sep = "\n")

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