This package enables the unification of results from different software performing the same analysis. It is designed with Plasmodium falciparum genomic data analysis in mind, but can be used for any kind of data. The tool has taken inspiration from the hAMRonization package.
pip install git+https://github.com/jodyphelan/etu.git
etu COI PyMOI <input_file> <unified_format_output>
Each analysis type must be implemented as a submodule of the package with the following objects defined:
- An abstract base class
Interface
defined ininterface.py
- A pydantic data model for the unified format defined in
interfact.py
which defines the fields that are required for each analysis.
The interface class must define the following methods:
write_result
which takes the unified format and writes it to a file.add_subparser
which takes a subparser and adds the analysis specific arguments to it.
Each software wihtin an analysis type must be implemented as a subclass inheriting from Interface
for each software that defines the parse
method. (see (pyMOI)[https://github.com/jodyphelan/etu/blob/main/src/etu/coi/pyMOI.py] for an example).