Library with useful tools for processing genomic data
Project description
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
Project details
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