Metadata-Version: 2.4
Name: genomicsdb
Version: 0.1.6
Summary: Python Bindings for querying GenomicsDB
Author: GenomicsDB.org
Author-email: support@genomicsdb.org
Maintainer: GenomicsDB.org
Maintainer-email: support@genomicsdb.org
License: MIT
Keywords: genomics,genomicsdb,variant,vcf,variant calls
Classifier: Development Status :: 5 - Production/Stable
Classifier: Intended Audience :: Developers
Classifier: Intended Audience :: Information Technology
Classifier: Intended Audience :: Science/Research
Classifier: License :: OSI Approved :: MIT License
Classifier: Topic :: Software Development :: Libraries :: Python Modules
Classifier: Operating System :: POSIX :: Linux
Classifier: Operating System :: MacOS :: MacOS X
Classifier: Programming Language :: Python :: 3.9
Classifier: Programming Language :: Python :: 3.10
Classifier: Programming Language :: Python :: 3.11
Classifier: Programming Language :: Python :: 3.12
Requires-Python: >=3.9
Description-Content-Type: text/markdown
License-File: LICENSE
Requires-Dist: numpy<2.0.0,>=1.24.0
Requires-Dist: pandas>=2.1.0
Requires-Dist: protobuf>=4.21.1
Requires-Dist: pyarrow>=14.0.0
Dynamic: author
Dynamic: author-email
Dynamic: classifier
Dynamic: description
Dynamic: description-content-type
Dynamic: keywords
Dynamic: license
Dynamic: license-file
Dynamic: maintainer
Dynamic: maintainer-email
Dynamic: requires-dist
Dynamic: requires-python
Dynamic: summary

[![License: MIT](https://img.shields.io/badge/License-MIT-yellow.svg)](https://opensource.org/licenses/MIT)
[![pypi](https://img.shields.io/pypi/v/genomicsdb.svg)](https://pypi.org/project/genomicsdb/) 

# GenomicsDB-Python
Python 3 Bindings to the native [GenomicsDB](https://github.com/GenomicsDB/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](https://github.com/GenomicsDB/GenomicsDB-Python/blob/master/genomicsdb/scripts/README.md). The available scripts are `genomicsdb_query` and `genomicsdb_cache` with the supported output options being csv, json and parquet files.

## Development
See [instructions](https://github.com/GenomicsDB/GenomicsDB-Python/blob/master/INSTALL.md) for local builds and running tests.
