#' @title Retrieve file names of files genereated by LTRpred
#' @description Useful helper function to generate automated file names
#' when crawling LTRpred generated result folders.
#' @param LTRpred.folder path to a \code{\link{LTRpred}} generated folder.
#' @param ws.wrap shall white space separated path names be wrapped with \code{'file name'}.
#' @author Hajk-Georg Drost
#' @examples
#' # without wrapped whitespaces
#' get.pred.filenames("path/to/LTRpred.folder")
#'
#' # with wrapped whitespaces
#' get.pred.filenames("path to/LTRpred.folder", ws.wrap = TRUE )
#' @export
get.pred.filenames <- function(LTRpred.folder, ws.wrap = FALSE){
folder.name <- basename(LTRpred.folder)
folder.name <- stringr::str_replace(folder.name,"_ltrpred","")
ltrdigest.folder <- paste0(folder.name,"_ltrdigest")
pred.files <- c(
file.path(LTRpred.folder,paste0(folder.name,"_LTRpred_DataSheet.tsv")),
file.path(LTRpred.folder,paste0(folder.name,"_LTRpred.bed")),
file.path(LTRpred.folder,paste0(folder.name,"_LTRpred.gff")),
file.path(LTRpred.folder,paste0(folder.name,"_ORF_prediction_nt.fsa")),
file.path(LTRpred.folder,paste0(folder.name,"-ltrdigest_complete.fas_CLUSTpred.blast6out")),
file.path(LTRpred.folder,paste0(folder.name,"-ltrdigest_complete.fas_CLUSTpred.log")),
file.path(LTRpred.folder,paste0(folder.name,"-ltrdigest_complete.fas_CLUSTpred.uc")),
file.path(LTRpred.folder,paste0(folder.name,"-ltrdigest_complete.fas_nt.fsa")),
file.path(LTRpred.folder,ltrdigest.folder,paste0(folder.name,"-ltrdigest_3ltr.fas")),
file.path(LTRpred.folder,ltrdigest.folder,paste0(folder.name,"-ltrdigest_5ltr.fas")),
file.path(LTRpred.folder,ltrdigest.folder,paste0(folder.name,"-ltrdigest_5ltr.fas")),
file.path(LTRpred.folder,ltrdigest.folder,paste0(folder.name,"_LTRdigestPrediction.gff")),
file.path(LTRpred.folder,ltrdigest.folder,paste0(folder.name,"-ltrdigest_tabout.csv")),
file.path(LTRpred.folder,ltrdigest.folder,paste0(folder.name,"-ltrdigest_complete.fas")),
file.path(LTRpred.folder,ltrdigest.folder,paste0(folder.name,"-ltrdigest_conditions.csv")),
file.path(LTRpred.folder,ltrdigest.folder,paste0(folder.name,"-ltrdigest_pbs.fas")),
file.path(LTRpred.folder,ltrdigest.folder,paste0(folder.name,"-ltrdigest_ppt.fas")),
file.path(LTRpred.folder,ltrdigest.folder,paste0(folder.name,"-ltrdigest_pbs.fas")))
if (ws.wrap){
pred.files <- ws.wrap.path(pred.files)
}
return(pred.files)
}
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