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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)