diagho-toolkit 0.1.1

Library with useful tools for processing genomic data

Diagho Toolkit

What is Diagho Toolkit ?

Diagho Toolkit is a python library which will read and parse a genomic file and return a generator with a pydantic model.

What database is used ?

• OMIM
• HGNC
• HPO
• gnomAD
• gnomAD constraint
• VCF
• Fasta
• GFF3

What pydantic model is returned ?

• Clinvar
• Feature
• Gene
• GnomAD
• GnomAD_constraint
• Pathology
• Region
• Sequence
• Symptom
• Variant

Installation

Install diagho-toolkit in pip

pip install diagho-toolkit

In your app if you want to parse a GFF3 file and get regions, you just need to call this method

from diagho_toolkit.gff3 import get_regions

get_regions(gff3_filename="gff3_file_path")

And this method will return a Generator with a list of RegionModel that you can easily save into your database.

Customize diagho-toolkit

Clone the project from github

Build and run the docker image

make docker

Into the container update and install requirements

make requirements
make install

Customize the project in the repository src/diagho_toolkit

Create and run tests

make tests

Update documentation in README.md and CHANGELOG.md and version in pyproject.toml

Leave the container and commit your release into github

git commit -am 'New commit'
git push 

Update the version in test-PyPI in github-actions with the workflow Test PyPi.

When all is ready, run the workflow Pypi to update the official new version