convAST

CLI tool to convert antibiotic susceptibility test (AST) results from lab devices, EMRs, LIMs to the an INSDC compatible format.

Installation

pip install convast

Usage

convast --output <output_file> --format <format> <input_file> 

Supported Formats

• Vitek
• Microscan
• Phoenix
• Sensititre

EMR/LIMs exports?

Program Structure

• Import a user-supplied tabular dataformat from args.input
• Import the yml formatted INSDC combined specification from linkML
• Apply a set of mappings based on args.format to the parsed tabular data
• Export the mapped data to the INSDC format to args.output

Core data/object model

• Standardised INSDC AST format dataclass imported from linkML (e.g., linkML documentation example)
• Input parent class with generic functions for parsing, iterating, write, applying mappings (e.g., hAMRonizedResultIterator)
• For each Vitek/Phoenix/Microtitre etc an iterator subclass that inherits from this input parent class including specific mappings and any adjustments to generic functions needed (e.g., tool specific hAMRonization classes)