R/check_bins.R

In methrix: Fast and efficient summarization of generic bedGraph files from Bisufite sequencing

# check_bedtools <- function(path = NULL) {
#
#     if (is.null(path)) {
#         check <- as.character(Sys.which(names = "bedtools"))[1]
#     } else {
#         check <- paste0(path, "/bedtools")
#         if (!file.exists(check)) {
#             stop("Could not locate bedtools at ", check, "\nDownload bedTools: <http://code.google.com/p/bedtools/>")
#         }
#     }
#
#     if (check != "") {
#         return(check)
#     } else {
#         stop("Could not locate bedtools at ", check, "\nDownload bedTools: <http://code.google.com/p/bedtools/>")
#     }
# }
#
# #---------------------------------------------------------------------------------------------------------------
#
# check_bedGraphToBigWig <- function(path = NULL) {
#
#     if (is.null(path)) {
#         check <- as.character(Sys.which(names = "bedGraphToBigWig"))[1]
#     } else {
#         check <- paste0(path, "/bedGraphToBigWig")
#         if (!file.exists(check)) {
#             stop("Could not locate bedGraphToBigWig at ", check, "\nDownload: <http://hgdownload.cse.ucsc.edu/admin/exe/>")
#         }
#     }
#
#     if (check != "") {
#         return(check)
#     } else {
#         stop("Could not locate bedGraphToBigWig at ", check, "\nDownload: <http://hgdownload.cse.ucsc.edu/admin/exe/>")
#     }
# }
#
#
# #---------------------------------------------------------------------------------------------------------------
#
# check_bedClip <- function(path = NULL) {
#
#     if (is.null(path)) {
#         check <- as.character(Sys.which(names = "bedClip"))[1]
#     } else {
#         check <- paste0(path, "/bedClip")
#         if (!file.exists(check)) {
#             stop("Could not locate bedClip at ", check, "\nDownload: <http://hgdownload.cse.ucsc.edu/admin/exe/>")
#         }
#     }
#
#     if (check != "") {
#         return(check)
#     } else {
#         stop("Could not locate bedClip at ", check, "\nDownload: <http://hgdownload.cse.ucsc.edu/admin/exe/>")
#     }
# }

#
# check_bins <- function(path = NULL, value=c("bedtools", "bedGraphToBigWig", "bedClip")){
#
#     names = match.arg(value)
#
#     if (is.null(path)) {
#         check <- as.character(Sys.which(names = names))[1]
#     } else {
#         check <- paste0(path, "/bedClip")
#         if (!file.exists(check)) {
#             stop("Could not locate ", names, " at ", check, "\nDownload: ",
#                  ifelse(names %in% c("bedCip", "bedGraphToBigWig"),
#                         "<http://hgdownload.cse.ucsc.edu/admin/exe/>",
#                         "<http://code.google.com/p/bedtools/>"))
#         }
#     }
#
#     if (check != "") {
#         return(check)
#     } else {
#         stop("Could not locate ", names," at ", check, "\nDownload: ",
#              ifelse(names %in% c("bedCip", "bedGraphToBigWig"),
#                     "<http://hgdownload.cse.ucsc.edu/admin/exe/>",
#                     "<http://code.google.com/p/bedtools/>"))
#     }
#
# }