predict_topology: Predict the topology of proteins from file

In pureseqtmr: Predict Transmembrane Protein Topology

Predict the topology of proteins from file

Description

Predict the topology of zero, one or more proteins, of which the names and sequences are stored in the FASTA format

Usage

predict_topology(
  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

a tibble with the columns 'name' and 'topology', where the 'name' column hold all the proteins' names, and 'topology' contains all respective topologies.

Note

unlike PureseqTM, the topologies predicted are returned in the same order as the original sequences. A bugreport is posted at the PureseqTM GitHub repository at https://github.com/PureseqTM/PureseqTM_Package/issues/11

Author(s)

Richèl J.C. Bilderbeek

See Also

use mock_predict_topology to do a mock prediction, as can be useful in testing

Examples

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

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