dmwg-data-pyutils

Data modeling WG Python CLI for data utils.

Install

It is always preferred to install within a virtual environment.

Requirements

• python >= 3.5

git clone [email protected]:COV-IRT/dmwg-data-pyutils.git
cd dmwg-data-pyutils
python3 -m virtualenv venv
source venv/bin/activate

pip install .

Usage

This tool has one entrypoint dmwg-data-pyutils with several subcommands.

ParseNextStrain

This subcommands parses the NextStrain JSON file into flat TSV collecting patient metadata and cummulative mutations.

dmwg-data-pyutils ParseNextStrain -h
usage: DMWG Data Utils ParseNextStrain [-h] [--json-path JSON_PATH] output

Extracts patient metadata, viral divergence, and viral mutations from the
nextstrain JSON file.

positional arguments:
  output                Path to output TSV file.

optional arguments:
  -h, --help            show this help message and exit
  --json-path JSON_PATH
                        Optional path to Nextstrain JSON. If it exists, then a
                        new version will not be downloaded from Nextstrain. If
                        it doesn't exist, the file will be downloaded to this
                        location. If no path is given, the JSON file will not
                        be saved locally.

How to add a new tool

• All new subcommands should be placed within dmwg_data_pyutils/subcommands
• Inherit from the abstract base class dmwg_data_pyutils.subcommands.Subcommand
• Add argument parser elements to classmethod __add_arguments__(cls, parser: ArgParserT)
• Add string description of tool functionality to classmethod __get_description__(cls)
• Define main tool logic in classmethod main(cls, options: NamespaceT)
• Add class import to dmwg_data_pyutils.subcommands.__init__
• Import class in dmwg_data_pyutils.__main__ (e.g., from dmwg_data_pyutils.subcommands import MyClass)
• Add subparsers in dmwg_data_pyutils.__main__.main(args=None, extra_subparser=None) (e.g., MyClass.add(subparsers=subparsers))
• Write tests please :-)

Note: The subcommand's class name will be used as the subcommand name