Add 'predict_topology_from_sequence' and 'predict_topologies_from_seq…

…uences'

DESCRIPTION

@@ -17,7 +17,7 @@ Imports:
  dplyr,
  ggplot2,
  plyr,
- pureseqtmr,
+ pureseqtmr (>= 1.3),
  purrr,
  rappdirs,
  readr,

NAMESPACE

@@ -29,7 +29,9 @@ export(parse_fasta_file)
 export(plot_locatome)
 export(plot_topology)
 export(plot_topology_text)
+export(predict_topologies_from_sequences)
 export(predict_topology)
+export(predict_topology_from_sequence)
 export(run_tmhmm)
 export(run_tmhmm_on_one_protein_fasta_file)
 export(run_tmhmm_on_sequence)

NEWS.md

@@ -6,6 +6,9 @@ Newest versions at top.
 
 ### NEW FEATURES
 
+ * Added `predict_topology_from_sequence` 
+ and `predict_topologies_from_sequences` to directly predict topologies
+ from protein sequences
  * Added dependency on `pureseqtmr`, 
  for `pureseqtmr::load_fasta_file_as_tibble`,
  which is approximately ten thousand times faster than `parse_fasta_file`

R/default_params_doc.R

@@ -14,6 +14,13 @@
 #' that contains one name and one sequence
 #' @param protein_sequence a protein sequence
 #' @param protein_sequences one or more protein sequences
+#' @param temp_fasta_filename filename to temporarily
+#' save the protein names and sequences.
+#' This file will be deleted when this
+#' function completed successfully
+#' @param temp_topology_filename filename to temporarily
+#' save the topology. This file will be deleted when this
+#' function completed successfully
 #' @param tmhmm_bin_filename path to the TMHMM binary file.
 #' Its default path can be ontained by using
 #' \link{get_default_tmhmm_bin_path}
@@ -45,6 +52,8 @@ default_params_doc <- function(
  one_protein_fasta_filename,
  protein_sequence,
  protein_sequences,
+ temp_fasta_filename,
+ temp_topology_filename,
  tmhmm_bin_filename,
  tmhmm_filename,
  tmhmm_result,

R/predict_topologies_from_sequences.R

@@ -0,0 +1,39 @@
+#' Run TMHMM directy on a protein sequence
+#' @inheritParams default_params_doc
+#' @return one or more topology sequences,
+#' for example \code{c("iiiimmmmooooo", "iiiii")}
+#' @seealso use \link{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)
+#' }
+#' @author Richèl J.C. Bilderbeek
+#' @export
+predict_topologies_from_sequences <- function(# nolint indeed a long function name
+ protein_sequences,
+ folder_name = get_default_tmhmm_folder(),
+ temp_fasta_filename = tempfile(fileext = ".fasta"),
+ temp_topology_filename = tempfile(fileext = ".topo")
+) {
+ t_sequences <- tibble::tibble(
+ name = paste0("protein_", seq_along(protein_sequences)),
+ sequence = protein_sequences
+ )
+ pureseqtmr::save_tibble_as_fasta_file(
+ t = t_sequences,
+ fasta_filename = temp_fasta_filename
+ )
+ t_topologies <- tmhmm::predict_topology(
+ fasta_filename = temp_fasta_filename,
+ folder_name = folder_name,
+ temp_topology_filename = temp_topology_filename
+ )
+ file.remove(temp_fasta_filename)
+ t_topologies$topology
+}

R/predict_topology.R

@@ -3,9 +3,6 @@
 #' @return a \link[tibble]{tibble} with the columns 'name'
 #' and 'topology', where the 'name' column hold all the proteins' names,
 #' and 'topology' contains all respective topologies.
-#' @param temp_topology_filename filename to temporarily
-#' save the topology. This file will be deleted when this
-#' function completed successfully
 #' @examples
 #' if (is_tmhmm_installed()) {
 #' fasta_filename <- system.file("extdata", "tmhmm.fasta", package = "tmhmm")

R/predict_topology_from_sequence.R

@@ -0,0 +1,30 @@
+#' Run TMHMM directy on a protein sequence
+#' @param protein_sequence a protein sequence, with
+#' the amino acids as capitals, for
+#' example \code{MEILCEDNTSLSSIPNSL}
+#' @inheritParams default_params_doc
+#' @return a topology sequence,
+#' for example \code{"iiiimmmmmoooo"}
+#' @examples
+#' if (is_tmhmm_installed()) {
+#' protein_sequence <- paste0(
+#' "QEKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLM",
+#' "SLAIADMLLGFLVMPVSMLTILYGYRWP"
+#' )
+#' predict_topology_from_sequence(protein_sequence)
+#' }
+#' @author Richèl J.C. Bilderbeek
+#' @export
+predict_topology_from_sequence <- function(
+ protein_sequence,
+ folder_name = get_default_tmhmm_folder(),
+ temp_fasta_filename = tempfile(fileext = ".fasta"),
+ temp_topology_filename = tempfile(fileext = ".topo")
+) {
+ tmhmm::predict_topologies_from_sequences(
+ protein_sequences = protein_sequence,
+ folder_name = folder_name,
+ temp_fasta_filename = temp_fasta_filename,
+ temp_topology_filename = temp_topology_filename
+ )
+}

tests/testthat/test-predict_topologies_from_sequences.R

@@ -0,0 +1,12 @@
+test_that("use", {
+ if (!is_tmhmm_installed()) return()
+ protein_sequences <- c(
+ "FAMILYVWFAMILYVW",
+ "FAMILYVWFAMILY"
+ )
+ topologies <- predict_topologies_from_sequences(
+ protein_sequences = protein_sequences
+ )
+ expect_equal(length(protein_sequences), length(topologies))
+ expect_equal(nchar(protein_sequences), nchar(topologies))
+})

tests/testthat/test-predict_topology_from_sequence.R

@@ -0,0 +1,13 @@
+test_that("use", {
+ if (!is_tmhmm_installed()) return()
+ protein_sequence <-
+ "QEKNWSALLTAVVIILTIAGNILVIMAVSLEKKLQNATNYFLMSLAIADMLLGFLVMPVSMLTILYGYRWP"
+ topology <- predict_topology_from_sequence(
+ protein_sequence = protein_sequence
+ )
+ expect_equal(
+ topology,
+ "iiiiiiMMMMMMMMMMMMMMMMMMMMMMMooooooooooooooMMMMMMMMMMMMMMMMMMMMMMMiiiii"
+ )
+ expect_equal(nchar(protein_sequence), nchar(topology))
+})