message('Loading R packages ... ')
suppressMessages(library("optparse"))
suppressMessages(library("rtracklayer"))
suppressMessages(library("HTSM"))
# sourceDir <- function(path, trace = TRUE, ...) {
# for (nm in list.files(path, pattern = '*.R')) {
# #if(trace) cat(nm,":")
# source(file.path(path, nm), ...)
# #if(trace) cat("/n")
# }
# }
# sourceDir(path = 'R',encoding = 'UTF-8')
option_list <- list(
make_option(opt_str = c('-g','--gtf'),help = 'The gtf file name to save.'),
make_option(opt_str = c('-b','--bed'),help = 'A bed file to convert gtf')
)
opt_parser <- OptionParser(option_list=option_list)
# print_help(opt_parser)
opt <- parse_args(opt_parser)
bed_file <- opt$bed
gtf_file <- opt$gtf
message('Converting the format')
gtf2bed(gtf2bed,bed_file = bed_file)
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