PubMLST API scraper

Description

This R script allows

• listing all of the available organisms on PubMLST API
• listing all of the available schemes for a given organisms (including dates of last changes to schemes and numbers of profiles included in each of the schemes)
• downloading specified scheme
• downloading specified scheme profiles

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

Rscript --vanilla pubMLST_scheme_scraper.R --help

To list available organisms on PubMLST

Rscript --vanilla pubMLST_scheme_scraper.R -f list_organisms

To list available schemes for a given organism

Rscript --vanilla pubMLST_scheme_scraper.R -f list_organism_schemes -o abaumannii

To download scheme profiles for a given organism and scheme ID

Rscript --vanilla pubMLST_scheme_scraper.R -f download_scheme_profiles -o abaumannii -s 1

To download scheme

Rscript --vanilla pubMLST_scheme_scraper.R -f download_scheme -o abaumannii -s 1