https://github.com/muhammedhasan/gnomad_rocksdb
https://github.com/muhammedhasan/gnomad_rocksdb
Last synced: 4 months ago
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- Host: GitHub
- URL: https://github.com/muhammedhasan/gnomad_rocksdb
- Owner: MuhammedHasan
- Created: 2022-01-03T05:05:02.000Z (over 4 years ago)
- Default Branch: master
- Last Pushed: 2024-08-01T04:17:09.000Z (almost 2 years ago)
- Last Synced: 2025-06-04T08:57:31.335Z (about 1 year ago)
- Language: Python
- Size: 12.7 KB
- Stars: 2
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.md
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README
# Gnomad Rocksdb
Fast look up interface allel frequency of variants from gnomad with rocksdb.
## Installation
```
conda install -c conda-forge python-rocksdb
pip install git+https://github.com/MuhammedHasan/gnomad_rocksdb.git
```
## Download database
Download rocksdb for gnomad
```console
gnomad_rocksdb_download --version {version} --db_path {output_path}
```
Supported version (4.1)
## Usage
```py
from gnomad_rocksdb import GnomadMafDB
db = GnomadMafDB(db_path)
db.get('17:1000:A>C')
# 0.001
db.get('chr17:1000:A>C')
# 0.001
db['17:1000:A>C']
# 0.001
'17:1000:A>C' in db
# True
```
## Create Database
```console
pip install tqdm snakemake more_itertools
# modify workflow/config.yaml
python -m snakemake -j 1
```