Python Bindings for querying GenomicsDB

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  • License: MIT License (MIT)
  • Author: GenomicsDB.org
  • Maintainer: GenomicsDB.org
  • Tags genomics , genomicsdb , variant , vcf , variant calls
  • Requires: Python >=3.9
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Project description

License: MIT pypi

GenomicsDB-Python

Python 3 Bindings to the native GenomicsDB library. Only queries are supported for now. For importing vcf files into GenomicsDB, use the command line tools - vcf2genomicsdb or gatk GenomicsDBImport.

Installation : Only Linux and MacOS are currently supported

Install genomicsdb binary wheels from PyPi with pip:

pip install genomicsdb

Or explicitly from a source distribution

# Download the source distribution from https://pypi.org/project/genomicsdb/#files as genomicsdb.source.tar.gz
tar xvf genomicsdb.source.tar.gz
cd genomicsdb-<version>
python setup.py install

GenomicsDB console scripts

See GenomicsDB query tool. The available scripts are genomicsdb_query and genomicsdb_cache with the supported output options being csv, json and parquet files.

Development

See instructions for local builds and running tests.

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Avatar for mlathara from gravatar.com mlathara Avatar for nalini from gravatar.com nalini

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  • License: MIT License (MIT)
  • Author: GenomicsDB.org
  • Maintainer: GenomicsDB.org
  • Tags genomics , genomicsdb , variant , vcf , variant calls
  • Requires: Python >=3.9
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