Variant Allele Frequency Lookup from gnomAD using RocksDB

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gnomad_rocksdb
gnomad_rocksdb
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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 

gnomad_rocksdb_download --version {version} --db_path {output_path}

Supported version (2.1.1, 3.1.2)

Usage 

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 

pip install tqdm kipoiseq snakemake cython cyvcf2
# modify workflow/config.yaml
python -m snakemake -j 1

Code Snippets

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import tarfile
import rocksdb


db = rocksdb.DB(snakemake.input['db'], rocksdb.Options())
backup = rocksdb.BackupEngine(snakemake.output['backup'])
backup.create_backup(db, flush_before_backup=True)

tar = tarfile.open(snakemake.output['backup_gzip'], "w:gz")
tar.add(snakemake.output['backup'], arcname="backup")
tar.close()
Python rocksdb From line 1 of workflow/backup_rocksdb.py 
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from tqdm import tqdm
import rocksdb
from kipoiseq.extractors import MultiSampleVCF


batch_size = snakemake.params['batch_size']
db = rocksdb.DB(snakemake.output['db'],
                rocksdb.Options(create_if_missing=True))

for vcf in snakemake.input['vcfs']:
    print('Processing %s' % vcf)
    vcf = MultiSampleVCF(vcf)

    for batch in tqdm(vcf.batch_iter(batch_size=batch_size)):
        batch_writer = rocksdb.WriteBatch()

        for v in batch:
            if v.info['AC'] > 0:
                af = v.info['AF']
                batch_writer.put(bytes(str(v).replace('chr', ''), 'utf-8'),
                                 bytes(str(af), 'utf-8'))
        db.write(batch_writer)
Python tqdm rocksdb kipoiseq From line 1 of workflow/create_rocksdb.py 
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run:
    shell("wget {params.url_vcf} -O {output.vcf}")
    shell("wget {params.url_tbi} -O {output.tbi}")
SnakeMake From line 31 of workflow/Snakefile 
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script:
    "./create_rocksdb.py"
SnakeMake From line 53 of workflow/Snakefile 
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script:
    "./backup_rocksdb.py"
SnakeMake From line 63 of workflow/Snakefile
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Created: 1yr ago
Updated: 1yr ago
Maitainers: public
URL: https://github.com/MuhammedHasan/gnomad_rocksdb
Name: gnomad_rocksdb
Version: 1
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Copyright: Public Domain
License: None
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