Building and querying clinvar

version: 0.1.1

Clinvar-build is a python module to build a SQLite database using the publicly available XML data from Clinvar. The module is slipped with command line entry points for routine queries.

The documentation for clinvar-build can be found here.

Installation

The package is available on PyPI, and conda, with the latest source code available on gitlab.

Installation using PyPI

To install the package from PyPI, run:

pip install clinvar-build

This installs the latest stable release along with its dependencies.

Installation using conda

A Conda package is maintained in my personal Conda channel. To install from this channel, run:

conda install afschmidt::clinvar-build

Installation using gitlab

If you require the latest updates, potentially not yet formally released, you can install the package directly from GitLab.

First, clone the repository and move into its root directory:

git clone git@gitlab.com:SchmidtAF/plot-misc.git
cd plot-misc

Install the dependencies:

# From the root of the repository
conda env create --file ./resources/conda/envs/conda_create.yaml

To add to an existing environment use:

# From the root of the repository
conda env update --file ./resources/conda/envs/conda_update.yaml

Next the package can be installed:

make install

Development

For development work, install the package in editable mode with Git commit hooks configured:

make install-dev

This command installs the package in editable mode and configures Git commit hooks, allowing you to run git pull to update the repository or switch branches without reinstalling.

Git Hooks Configuration

When setting up a development environment, the setup-hooks command configures Git hooks to enforce conventional commit message formatting and spell check using codespell.

To view the commit message format requirements, run:

./.githooks/commit-msg -help

For frequent use, add this function to your shell configuration (~/.bashrc or ~/.zshrc):

commit-format-help() {
    local git_root
    git_root=$(git rev-parse --show-toplevel 2>/dev/null)
    
    if [ -z "$git_root" ]; then
        echo "Error: Not inside a git repository"
        return 1
    fi
    
    local hook_path="$git_root/.githooks/commit-msg"
    
    if [ ! -f "$hook_path" ]; then
        echo "Error: commit-msg hook not found"
        return 1
    fi
    
    "$hook_path" --help
}

Validating the package

After installing the package from GitLab, you may wish to run the test suite to confirm everything is working as expected:

# From the root of the repository
pytest tests

Usage

Please have a look at the examples in resources for some possible recipes.