Database management pipelines

Below is a description of command line tools that the pdm_utils package contains to analyze and manipulate data within a MySQL database:

Some tools are bound to the most current schema version (“yes”), as they need to know where to find types of data in the database. Other tools (“no”), or sub-tools (“yes”/”no”), are schema-agnostic, and can be used for any type of MySQL database.

Most tools provide functionality without respect to SEA-PHAGES-specific assumptions or goals. Some tools are more oriented to the SEA-PHAGES program by providing (optional) interactions with PhagesDB or by encoding SEA-PHAGES-specific assumptions about the data. For instance, a series of evaluations are implemented in the import and compare pipelines to ensure data quality, and while some of these evaluations are SEA-PHAGES-specific, others are not.

• compare
• convert
• export
• find_domains
• freeze
• get_data
• get_db
• get_gb_records
• import
• phamerate
• push
• pham_review
• revise
• update

pdm_utils tools

Tool	Description	Schema bound	SEA-PHAGES oriented
compare	Directly compare phage data between a database instance, PhagesDB, and GenBank	Yes	Yes
convert	Upgrade or downgrade a database instance to another schema version	No	No
export	Export data from a database	Yes/No	No
find_domains	Identify NCBI conserved domains in genes	Yes	No
freeze	Create a derivative database instance that is no longer routinely updated	Yes	No
get_db	Retrieve the most up-to-date version of the database	No	No
get_data	Retrieve new data that needs to be imported or updated from PhagesDB and GenBank	Yes	Yes
get_gb_records	Retrieve GenBank records associated with genomes in the database	Yes	No
import	Import new or replacement genome annotations	Yes	Yes
phamerate	Group phage genes into phamilies based on amino acid sequence similarity	Yes	No
push	Push an updated database to a public server	No	No
review	Review gene description data consistency of a database	Yes	No
revise	Revise inconsistent data and prepare for submission to GenBank for updating records	Yes	No
update	Update specific fields	No	No

The pdm_utils toolkit can be used to manage different database instances. However, some tools may only be relevant specifically to the primary instance, Actino_Draft.