Create customized phage genomics databases

Below is a description of how the pdm_utils package can be used to create customized phage genomics databases using the same tools and pipelines implemented in the SEA-PHAGES program.

First, create a new, empty database with the most current database schema:

> python3 -m pdm_utils get_db PhageDatabase new

A new MySQL database, PhageDatabase, has been created, and it has the same structure as the most current Actino_Draft database.

Note

You may see two MySQL notices appear during installation: Warning: 3090, “Changing sql mode ‘NO_AUTO_CREATE_USER’ is deprecated. It will be removed in a future release.” Warning: 1305, “PROCEDURE test_empty.split_subcluster does not exist” These warnings can be ignored.

If a different schema version is needed, this can be selected at the time of installation:

> python3 -m pdm_utils get_db PhageDatabase new -s 7

Alternatively, the convert tool can be used to subsequently downgrade the schema to a prior version.

Next, use import to add new genomics data to PhageDatabase…