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.
Release files for genomicsdb 0.1.6
For a detailed explanation of source distributions (sdists) and built distributions (wheels), please see the package formats documentation.
Built distributions (wheels)
Total release size: 85.2 MB
Release files / genomicsdb-0.1.6-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | genomicsdb-0.1.6-cp312-cp312-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
|---|---|
| Size | 9.0 MB |
| Tags | CPython 3.12 Linux glibc 2.17+ x86-64 |
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| Download URL | genomicsdb-0.1.6-cp312-cp312-macosx_12_0_x86_64.whl |
|---|---|
| Size | 6.5 MB |
| Tags | CPython 3.12 macOS 12.0+ x86-64 |
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| Download URL | genomicsdb-0.1.6-cp312-cp312-macosx_12_0_arm64.whl |
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| Size | 5.8 MB |
| Tags | CPython 3.12 macOS 12.0+ ARM64 |
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twine/6.1.0 CPython/3.12.9
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Transparency logRelease files / genomicsdb-0.1.6-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | genomicsdb-0.1.6-cp311-cp311-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Size | 9.0 MB |
| Tags | CPython 3.11 Linux glibc 2.17+ x86-64 |
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| Download URL | genomicsdb-0.1.6-cp311-cp311-macosx_12_0_x86_64.whl |
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| Size | 6.5 MB |
| Tags | CPython 3.11 macOS 12.0+ x86-64 |
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| Download URL | genomicsdb-0.1.6-cp311-cp311-macosx_12_0_arm64.whl |
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| Size | 5.8 MB |
| Tags | CPython 3.11 macOS 12.0+ ARM64 |
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| Tags | CPython 3.10 Linux glibc 2.17+ x86-64 |
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| Download URL | genomicsdb-0.1.6-cp310-cp310-macosx_12_0_x86_64.whl |
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| Size | 6.5 MB |
| Tags | CPython 3.10 macOS 12.0+ x86-64 |
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| Download URL | genomicsdb-0.1.6-cp310-cp310-macosx_12_0_arm64.whl |
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| Size | 5.8 MB |
| Tags | CPython 3.10 macOS 12.0+ ARM64 |
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Transparency logRelease files / genomicsdb-0.1.6-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl
| Download URL | genomicsdb-0.1.6-cp39-cp39-manylinux_2_17_x86_64.manylinux2014_x86_64.whl |
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| Size | 9.0 MB |
| Tags | CPython 3.9 Linux glibc 2.17+ x86-64 |
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| Download URL | genomicsdb-0.1.6-cp39-cp39-macosx_12_0_x86_64.whl |
|---|---|
| Size | 6.5 MB |
| Tags | CPython 3.9 macOS 12.0+ x86-64 |
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| Download URL | genomicsdb-0.1.6-cp39-cp39-macosx_12_0_arm64.whl |
|---|---|
| Size | 5.8 MB |
| Tags | CPython 3.9 macOS 12.0+ ARM64 |
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twine/6.1.0 CPython/3.12.9
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