ImmuneDB is backed by a MySQL database that can be queried directly to gather information, bypassing the Python API.
There are many ways to access the database directly. The two introduced here
are directly through MySQL or using immunedb_sql
which simply wraps a call to
MySQL.
$ immunedb_sql PATH_TO_CONFIG
This is entirely equivalent to using mysql
and will drop to the MySQL
interpreter. You can also pass a query directly from the command line. For
example:
$ immunedb_sql PATH_TO_CONFIG --query 'select * from samples'
From the command line, you may access an ImmuneDB database DATABASE
from user
USERNAME
with:
$ mysql -u USERNAME -p DATABASE
This will prompt for a password and then to the database. This method of access
is useful for quickly querying the database. To save results of a query
QUERY
run the command:
$ mysql -u USERNAME -p DATABASE -e "QUERY" > output