Enterobase webpage scraper

Description:

This R script allows

• listing all of the available schemes on Enterobase
• listing all of the available organisms on Enterobase
• finding the date and time of the last change on scheme of interest
• downloading schemes from Enterobase

Requirements

• tidyverse
• rvest
• knitr
• optparse

In case you would like to use this script you can easily install all the required packages by running the code below in your R session:

# Listing required packages
required_packages <- c("tidyverse", "rvest", "knitr", "optparse")

# Check if required packages are installed
missing_packages <- setdiff(required_packages, installed.packages()[,"Package"])

# Install missing packages
if (length(missing_packages) > 0) {
  message("Installing missing packages: ", paste(missing_packages, collapse = ", "))
  install.packages(missing_packages)
}

Usage:

To see help

Rscript --vanilla enterobase_scheme_scraper.R --help

To list available organisms on Enterobase

Rscript --vanilla enterobase_scheme_scraper.R -f list_organisms

To list available schemes for given organism

Rscript --vanilla enterobase_scheme_scraper.R -f list_organism_schemes -o Salmonella

To download scheme

Rscript --vanilla enterobase_scheme_scraper.R -f download_scheme -o Salmonella -s Achtman7GeneMLST