cgMLST.org webpage scraper

Description

This R script allows

• listing all of the available cgMLST schemes on cgMLST.org
• finding the version and/or date and time of the last change on scheme of interest
• downloading specified schemes from cgMLST.org

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

The script can be used directly from command line.

To see help message

Rscript --vanilla cgMLSTorg_scheme_scraper.R --help

To list all available schemes on cgMLST.org

Rscript --vanilla cgMLSTorg_scheme_scraper.R

To finding the date and time of the last change on scheme of interest

Rscript --vanilla cgMLSTorg_scheme_scraper.R -f last_change -i Abaumannii

To download specific scheme

Rscript --vanilla cgMLSTorg_scheme_scraper.R -f download -i Abaumannii