derrick-daniel
/ CARD-DB_to_Abricate-CARD-DB_format
Last active
December 22, 2023 15:04
This script is tailored for the manipulation of the Comprehensive Antibiotic Resistance Database (CARD). It functions by ingesting data from a JSON file, selectively extracting pertinent details, and then reformatting them to align with the Abricate CARD DB structure. This process is essential for updating the Abricate CARD DB.
This file contains hidden or bidirectional Unicode text that may be interpreted or compiled differently than what appears below. To review, open the file in an editor that reveals hidden Unicode characters.
Learn more about bidirectional Unicode characters
| import json | |
| def format_sequence(sequence): | |
| return '\n'.join([sequence[i:i+60] for i in range(0, len(sequence), 60)]) | |
| def process_category_name(name): | |
| words = name.split() | |
| if words[-1].lower() == 'antibiotic': | |
| return ' '.join(words[:-1]) | |
| return ' '.join(words) |