Python Bindings for querying GenomicsDB

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Project description

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.

Project details

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Release history Release notifications | RSS feed

0.1.6

Mar 23, 2025

0.1.5

Mar 20, 2025

0.1.4

Mar 14, 2025

0.1.3

Feb 20, 2025

0.1.2

Feb 18, 2025

0.1.1

Feb 12, 2025

0.1.0

Jan 30, 2025

This version

0.0.9.19.dev1 pre-release

Jan 30, 2025

0.0.9.19.dev0 pre-release

Jan 28, 2025

0.0.9.18

Dec 19, 2024

0.0.9.17

Dec 16, 2024

0.0.9.17.dev5 pre-release

Dec 3, 2024

0.0.9.17.dev4 pre-release

Oct 1, 2024

0.0.9.17.dev3 pre-release

Oct 1, 2024

0.0.9.17.dev2 pre-release

Oct 1, 2024

0.0.9.17.dev1 pre-release

Oct 1, 2024

0.0.9.17.dev0 pre-release

Sep 24, 2024

0.0.9.16

Sep 6, 2024

0.0.9.15

Jul 18, 2024

0.0.9.14

Jul 3, 2024

0.0.9.14.dev1 pre-release

Oct 1, 2024

0.0.9.14.dev0 pre-release

Jul 18, 2024

0.0.9.13

May 13, 2024

0.0.9.12

May 7, 2024

0.0.9.11

Apr 18, 2024

0.0.9.10

Feb 28, 2024

0.0.9.9

Feb 27, 2024

0.0.9.8

Feb 10, 2024

0.0.9.7

Jan 10, 2024

0.0.9.6

Dec 13, 2023

0.0.9.5

Dec 13, 2023

0.0.9.4

Dec 7, 2023

0.0.9.3

Nov 17, 2023

0.0.9.2

Oct 10, 2023

0.0.9.1

Oct 4, 2023

0.0.9.0

Oct 3, 2023

0.0.8.0

Oct 2, 2023

0.0.7.0

Jul 10, 2020

0.0.6.4

May 29, 2020

0.0.6.1

May 29, 2020

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Uploaded Jan 30, 2025 CPython 3.12macOS 12.0+ ARM64

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