#' Connect and parse UniProt Family Domains information.
#'
#' The function is work to retrieve Family Domains data from UniProt for a
#' list of proteins accessions.For more information about what included
#' in the Family Domains data see https://www.uniprot.org/help/return_fields.
#'
#' @usage GetFamily_Domains(ProteinAccList , directorypath = NULL)
#'
#' @param ProteinAccList Vector of UniProt Accession/s
#'
#' @param directorypath path to save excel file containig results returened by the function.
#'
#' @return DataFrame where rows names are the accession
#' and columns contains the information retrieved from the UniProt
#'
#' @note The function also, Creates a csv file with the retrieved information.
#'
#' @export
#'
#' @author Mohmed Soudy \email{Mohamed.soudy@57357.com} and Ali Mostafa \email{ali.mo.anwar@std.agr.cu.edu.eg}
GetFamily_Domains<- function(ProteinAccList , directorypath = NULL){
if(!has_internet())
{
message("Please connect to the internet as the package requires internect connection.")
return()
}
message("Please wait we are processing your accessions ...")
pb <- progress::progress_bar$new(total = length(ProteinAccList))
# Family_Domains information to be collected
columns <- c("cc_domain,protein_families,ft_coiled,ft_compbias,ft_domain,ft_motif,ft_region,ft_repeat,ft_zn_fing")
baseUrl <- "https://rest.uniprot.org/uniprotkb/search?query=accession:"
ProteinInfoParsed_total = data.frame()
for (ProteinAcc in ProteinAccList)
{
#to see if Request == 200 or not
Request <- tryCatch(
{
GET(paste0(baseUrl , ProteinAcc,"&format=tsv") , timeout(5))
},error = function(cond)
{
message("Internet connection problem occurs and the function will return the original error")
message(cond)
}
)
#this link return information in tab formate (format = tab)
#columns = what to return from all of the information (see: https://www.uniprot.org/help/uniprotkb_column_names)
ProteinName_url <- paste0(ProteinAcc,"&format=tsv&fields=",columns)
RequestUrl <- paste0(baseUrl , ProteinName_url)
RequestUrl <- URLencode(RequestUrl)
if (length(Request) == 0)
{
message("Internet connection problem occurs")
return()
}
if (Request$status_code == 200){
# parse the information in DataFrame
ProteinDataTable <- tryCatch(read.csv(RequestUrl, header = TRUE, sep = '\t'), error=function(e) NULL)
if (!is.null(ProteinDataTable))
{
ProteinDataTable <- ProteinDataTable[1,]
ProteinInfoParsed <- as.data.frame(ProteinDataTable,row.names = ProteinAcc)
# add Dataframes together if more than one accession
ProteinInfoParsed_total <- rbind(ProteinInfoParsed_total, ProteinInfoParsed)
}
}else {
HandleBadRequests(Request$status_code)
}
pb$tick()
}
if(!is.null(directorypath))
{
write.csv(ProteinInfoParsed_total , paste0(directorypath , "/" , "Family_Domains Information.csv"))
}
return(ProteinInfoParsed_total)
}
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