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)

Using the linkml runtime - the dataclasses are generated as follows:

gen-python convast/schema/NCBI_schema.yaml > convast/schema.py