SpliceAI Variant Lookup and Prediction with RocksDB

public 1yr ago Version: v1.0.0 0 bookmarks

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Fast look up interface and prediction for missing variants in look table for spliceAI with rocksdb.

Installation

Clone this git repository:

Code Snippets

import tarfile
import rocksdb


db = rocksdb.DB(snakemake.input['db'], 
                rocksdb.Options(max_open_files=5000), 
                read_only=True)
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 scripts/backup_rocksdb.py

from spliceai_rocksdb.create import create_spliceai_rocksdb


vcfs = [
    snakemake.input['snv'],
    snakemake.input['indel']
]
create_spliceai_rocksdb(snakemake.output['db'], vcfs,
                        batch_size=snakemake.params['batch_size'])

Python SpliceAI Rocksdb From line 1 of scripts/create_rocksdb.py

from spliceai_rocksdb.spliceAI import SpliceAI


if snakemake.params['lookup_only']:
    model = SpliceAI(db_path=snakemake.params['db_path'])
else:
    model = SpliceAI(snakemake.input['fasta'],
                     annotation=snakemake.params['genome'],
                     db_path=snakemake.params['db_path'])


model.predict_save(snakemake.input['vcf'],
                   snakemake.output['csv'])

Python SpliceAI Rocksdb From line 1 of scripts/predict.py

shell:
    "wget -O - {params} | gunzip -c > {output}"

SnakeMake From line 30 of workflow/Snakefile

shell:
    "bcftools view -O z -o {output.indel_by_chr} {input.indel} --regions {wildcards.chromosome}"

SnakeMake BCFtools From line 38 of workflow/Snakefile

shell:
    "bcftools view -O z -o {output.snv_by_chr} {input.snv} --regions {wildcards.chromosome}"

SnakeMake BCFtools From line 46 of workflow/Snakefile

script:
    "./scripts/create_rocksdb.py"

SnakeMake From line 58 of workflow/Snakefile

script:
    "./scripts/backup_rocksdb.py"

SnakeMake From line 68 of workflow/Snakefile

script:
    "./scripts/predict.py"

SnakeMake From line 98 of workflow/Snakefile

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Created: 1yr ago

Updated: 1yr ago

Maitainers: public

URL: https://github.com/gagneurlab/spliceai_rocksdb

Name: spliceai_rocksdb

Version: v1.0.0

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License: None

Keywords:

BCFtools Snakemake rocksdb SpliceAI Rocksdb Genetic variation

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