EBISearchMatadata

This pipeline allows to extract metadata in the biosamples domain by default.

Installation

• git clone https://github.com/KhadimGueyeKGY/EBISearchMatadata.git

Usage:

for help or to know how to use this script type:

python EBISearchMatadata.py 

• By default :

  • Domain: biosamples
  • Fileds: id,name,collection_date

NB: you don't need to write it (damine and fields) if you don't change domain or fields.

Example:

 python EBISearchMatadata_v2.py --input ../input/hse_pathogens.fungi_w_taxa.json

Output

After execution of the code, three files will be created in the same directory as the input file:

• <file>_N*.xml : containing the metadata
• <file>_request_url_N*.txt : containing the url
• <file>_request_curl_N*.txt : containing the command line