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.
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| 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) |