@@ -8,7 +8,7 @@ Description: Plots protein properties and visualizes position of peptide immunog

     suitability for antibody-based methods aiming to detect native proteins.

 License: Apache License (>= 2)

 Encoding: UTF-8

-LazyData: true

+LazyData: false

 Config/testthat/edition: 3

 RoxygenNote: 7.3.1

 VignetteBuilder: knitr

@@ -18,7 +18,8 @@ Imports:

     ggplot2,

     httr,

     jsonlite,

-    patchwork

+    patchwork,

+    UniProt.ws

 Suggests: 

     BiocStyle,

     knitr,

@@ -7,5 +7,6 @@ export(plotImmunogen)

 export(plotProtein)

 export(removeImmunogen)

 export(renameImmunogen)

+import(UniProt.ws)

 import(ggplot2)

 import(patchwork)

@@ -1,34 +1,36 @@

 #' Retrieve structural and functional features to create a protein DataFrame

 #'

 #' @param uniprot String, UniProt ID

+#' @param taxId Integer, Taxonomy species ID

 #'

 #' @description

-#' By providing a valid UniProt ID, information from UniProt (https://www.uniprot.org/) and PredictProtein (https://predictprotein.org/) is queried via their

-#' respective APIs. The retrieved information regarding secondary structure, solvent accessibility, membrane

-#' regions, protein-binding regions, disordered regions, PTMs and disulfide bridges is saved per residue

-#' within a Protein DataFrame. After calling `getProteinFeatures()`, immunogens can be added to the Protein

-#' DataFrame.

+#' By providing a valid UniProt ID, information from UniProt (https://www.uniprot.org/) and PredictProtein

+#' (https://predictprotein.org/) is queried via their respective APIs. The retrieved information regarding

+#' secondary structure, solvent accessibility, membrane regions, protein-binding regions, disordered regions,

+#' PTMs and disulfide bridges is saved per residue within a Protein DataFrame.

+#' After calling `getProteinFeatures()`, immunogens can be added to the Protein DataFrame.

 #'

 #' @return Protein DataFrame

 #' @export

 #'

+#' @import UniProt.ws

+#'

 #' @examples getProteinFeatures("P55087")

-getProteinFeatures <- function(uniprot) {

+getProteinFeatures <- function(uniprot, taxId = 9606) {

-  # check if Uniprot ID is valid

+  # check if UniProt ID is valid

   if (is.character(uniprot) == FALSE) {

     stop("Please provide a UniProt ID.")

   }

   # retrieve results from UniProt

-  resultUniprot <- accessUniprot(uniprot)

-  uniprotDF <- resultUniprot$features

+  uniprotDF <- accessUniprot(uniprot, taxId=9606)

   # retrieve results from PredictProtein

   predictProteinDF <- accessPredictProtein(uniprot)

   # retrieve protein sequence

-  seq <- getProteinSequence(resultUniprot)

+  seq <- uniprotDF$Sequence

   # create feature dataframe

   df <- createFeatureDataFrame(uniprot, seq, uniprotDF, predictProteinDF)

@@ -38,24 +40,16 @@ getProteinFeatures <- function(uniprot) {

 }

-accessUniprot <- function(uniprot) {

-

-  # create protein-specific UniProt URL

-  url <- paste0("https://www.uniprot.org/uniprot/", uniprot, ".json")

-

-  # make GET request

-  response <- httr::GET(url = url)

+accessUniprot <- function(uniprot, taxId) {

-  # check if request was successful

-  if (response$status_code == 200) {

+  # create UniProt interface

+  up <- UniProt.ws(taxId=taxId)

-    # parse JSON response

-    result <- jsonlite::fromJSON(httr::content(response, "text", encoding="UTF-8"))

-    return(result)

+  # retrieve sequence, PTM and disulfide bridge information

+  result <- select(up, keys=uniprot, columns=c("sequence", "ft_disulfid", "ft_mod_res", "ft_lipid", "ft_carbohyd"),

+    keytype="UniProtKB")

-  } else {

-    stop(c("Error fetching data from Uniprot for ", uniprot))

-  }

+  return(result)

 }

@@ -80,22 +74,6 @@ accessPredictProtein <- function(uniprot) {

 }

-getProteinSequence <- function(result) {

-

-  if (is.list(result) == FALSE) {

-    stop("Expected a list.")

-  }

-

-  seq <- as.character(result$sequence$value)

-

-  if (is.character(seq) == FALSE || length(seq) == 0) {

-    stop("Expected a character.")

-  }

-

-  return(seq)

-}

-

-

 createFeatureDataFrame <- function(uniprot, seq, uniprotDF, predictProteinDF) {

   # create vectors of positions and residues

@@ -127,11 +105,11 @@ createFeatureDataFrame <- function(uniprot, seq, uniprotDF, predictProteinDF) {

   proteinDF <- addPositions(proteinDF, disorderVector, "Disorder")

   # PTMs (UniProt)

-  PTMVector <- retrieveSinglePositions(uniprotDF, c("Modified residue", "Lipidation", "Glycosylation"))

+  PTMVector <- retrievePTMPositions(uniprotDF, c("Modified.residue", "Lipidation", "Glycosylation"))

   proteinDF <- addPositions(proteinDF, PTMVector, "PTM")

   # disulfide bridges (UniProt)

-  disulfideBridgeVector <- retrieveSinglePositions(uniprotDF, c("Disulfide bond"))

+  disulfideBridgeVector <- retrieveDisulfidePositions(uniprotDF$Disulfide.bond)

   proteinDF <- addPositions(proteinDF, disulfideBridgeVector, "disulfideBridge")

   return(proteinDF)

@@ -154,15 +132,66 @@ collectRegionPositions <- function(start, end) {

 }

-retrieveSinglePositions <- function(uniprotDF, columns) {

+retrieveDisulfidePositions <- function(column) {

-  # filter for relevant rows in Uniprot dataframe

-  filteredDF <- uniprotDF[uniprotDF$type %in% columns, ]

+  positions <- numeric()

+

+  annotations <- unlist(strsplit(column, ";"))

+

+  for (annot in annotations) {

+

+    if (grepl("\\.\\.", annot)) {

-  # collect all start and end positions of PTM and disulfide bridge annotations

-  singlePositionsVector <- sort(c(filteredDF$location$start$value, filteredDF$location$end$value))

+      range <- unlist(strsplit(annot, "\\.\\.")) # escaping the dot character for correct string splitting

+

+      start <- as.integer(gsub("[^0-9-]", "", range[1]))

+      end <- as.integer(range[2])

+

+      positions <- c(positions, start, end)

+

+    } else {

+

+      next

+    }

+  }

+

+  return(sort(positions))

+}

+

+

+retrievePTMPositions <- function(df, columns) {

+

+  positions <- numeric()

+

+  for (column in columns) {

+

+    # skip empty values

+    if (is.na(df[[column]])) {

+

+      next

+

+    } else {

+

+      annotations <- unlist(strsplit(df[[column]], ";"))

+

+      for (annot in annotations) {

+

+        # skip note and evidence strings

+        if (grepl("\\/", annot)) {

+

+          next

+

+        } else {

+

+          position <- as.integer(gsub("[^0-9-]", "", annot))

+          positions <- c(positions, position)

+

+        }

+      }

+    }

+  }

-  return(singlePositionsVector)

+  return(sort(positions))

 }

@@ -4,7 +4,7 @@

 \alias{getProteinFeatures}

 \title{Retrieve structural and functional features to create a protein DataFrame}

 \usage{

-getProteinFeatures(uniprot)

+getProteinFeatures(uniprot, taxId = 9606)

 }

 \arguments{

 \item{uniprot}{String, UniProt ID}

@@ -6,6 +6,7 @@ test_that("Only strings are accepted as input", {

 test_that("Dataframe is returned if successul", {

   expect_s3_class(getProteinFeatures("P55087"), "data.frame")

+  expect_s3_class(getProteinFeatures("Q9NZC2"), "data.frame")

 })