TumbleOwlee/ifhutil

R utility package

R Package ifhutil

This repository contains sources of the ifhutil package. This packages provides various utility function to simplify scripts while also providing an clean and pretty format of output messages.

Quickstart

You can install this package easily using remotes::install_github(..) by executing the following command.

remotes::install_github("tumbleowlee/ifhutil")

See man page for documentation of all provided functions.

Example

# Encapsule the main routine for pretty warnings/errors
main <- function() {
    # Initialize and install dependencies.
    ifh.info('Check and install missing dependencies...')
    ifh.init(c('numbers'), quiet = TRUE)

    # Setup CLI argument parser
    option_list = list(
        make_option(c('--annotated'), type = 'character', default = config$annotated,
                    help = 'eggNog-mapper annotation output file (e.g. out.emapper.annotations).', metavar = 'FILE'),
        make_option(c('--quiet'), action = 'store_true', default = config$quiet, help = 'Suppress all output.')
    )
    opt_parser = OptionParser(description = 'Generates GENEID-GO and GENEID-KEGG_ko mappings based on eggNog-mapper output.', option_list = option_list)
    # This also prints the user inputs to provide the user the option to verify
    opt = ifh.parse_args(opt_parser)

    <do-something>
}

# Execute `main()` with prettified log
ifh.run({main()})