beacon_api.utils.db_load

Beacon Database Loader.

This utility script is used to parse VCF files into a PostgreSQL database. See Database table beacon_data_table for what information is extracted from the VCF file.

Datafiles *.vcf are denoted as datafile in the script parameters. Metadata for a datafile is given in a *.json file, denoted as metafile in the script parameters.

Note

Future releases are expected to drop the additional metafile parameter in favour of simplifying the database loading process, reading metadata from the datafile(s) directly.

Environment Setup

Location of the table creation script can be changed with the TABLES_SCHEMA environment variable.

ENV	Default	Description
TABLES_SCHEMA	data/init.sql	Database tables schema for metadata and variants.

Run Module

Below are the two ways of running this module (pip installed and uninstalled).

$ beacon_init [datafile] [metafile]
$ python -m beacon_api.utils.db_load [datafile] [metafile]

Note

This script has been tested with VCF specification v4.2.

Functions

init_beacon_db([arguments])	Run database operations here.
main()	Run the beacon_init script.
parse_arguments(arguments)	Parse command line arguments.

Classes

BeaconDB()

Database connection and operations.