Antibiogram NCBI Biosample scraper

Given a set of NCBI Biosample ids, this script check the corresponding html page for antibiogram table, storing it as a JSON file in a separate folder

In order to run this script you need some dependencies. To sort this out quickly, the use of pipenv is encouraged. Follow the tutorial on pipenv site to install pipenv, or provide the dependencies for the script by yourself.

To create a virtualenv and install the dependencies do:

pipenv install --three

Note: The file is written in Pyhton 3

To activate the virtual environment do:

pipenv shell

For information about the script, just use the --help command:

python amr_downloader.py --help

The script can be run without any paramters, it will read the accessions from the ncbi_accessions.txt file and store the results in the files directory. If for some reason the process is interrupted, you can provide also a first_acc argument to start the extraction process from the corresponding accession.