This package provides a variety of commands for manipulating different types of common outputs (e.g. mafs, vcf and txt files) from different bioinformatic variant callers such as mutect and vardict.
Supported File Types:
For general use you can run: pip install postprocessing_variant_calls or a tagged version with pip install git+https://github.com/msk-access/postprocessing_variant_calls.git@<version>
For setting up a development environment please see the section.
See for commmand line usage of the package.
Have an environment with python >= 3.8 installed.
Install poetry:
Then install project dependencies with Poetry.
To access the environment after initial setup up run:
The Gitbook for this repository is configured so changes are written in Gitbook and synced with the docs branch.
To contribute to the documentation, you can write your changes in , request a review, and merge the changes. Keep in mind, you will need access to the organization to contribute.
Each file-type supported should have a section in the Gitbook detailing the implementation of the file-type and a justification of it's operations. For example, the maf file-type has it's own section, which includes a description of how a maf is defined internally in the package and a justification of it's operations and how to use them.
Beyond file-type sections, you will also notice a section called cli, which lists all commands in the postprocessing_variant_calls package. Do not manually edit this section. This section is created using the typer-cli package, which uses the typer help parameters specified in typer commands to generate documentation. It is automatically updated by the git-action, .github/workflows/document_package.yml upon a push to the main branch. To make sure the cli.md document updates to include newly added commands, specify all relevant typer help parameters.
If you'd like to see a mock of your typer commands as they'll appear in the cli.md document, you can run: poetry run typer postprocessing_variant_calls.main utils docs > docs/cli.md in a properly configured dev environment. Note that this file should not be included in your PRs. The cli.md should be only updated through the git-action, .github/workflows/document_package.yml.
pip install poetrycd /path/to/postprocessing_variant_calls
poetry install .poetry shell