update: make updates to specific database fields

Sometimes it is necessary to modify or update specific fields for specific phages. This can be accomplished using the pdm_utils update tool that relies on a specifically structured update ticket (Update tickets):

> python3 -m pdm_utils update Actino_Draft -f ./update_table.csv -c config_file.txt

The argument ‘Actino_Draft’ indicates the name of the database in which the updates should be implemented. The ‘./update_table.csv’ indicates the CSV-formatted table containing the list of update tickets. Each ticket is implemented with very little QC. As with other pipelines, use of the Database management configuration file option can automate accessing MySQL.

Additionally, update can be used to quickly increment the database version, which needs to be changed every time changes are made in the database:

> python3 -m pdm_utils update Actino_Draft -v