Python API

OakVar functionality is available through Python API. For example, OakVar's annotation pipeline can be started with the following:

>>> import oakvar as ov
>>> ov.api.run(inputs=["input.vcf"], annotators=["clinvar"], report_types=["vcf"])

There is 1 to 1 correspondence between command-line interface commands and Python API functions. The table below shows such correspondence.

CLI	Python API	Functionality
ov config system	oakvar.api.config.system	Gets or sets system configuration.
ov config user	oakvar.api.config.user	Gets user configuration.
ov issue	oakvar.api.report_issues	Opens a webpage to report OakVar issues.
ov license	oakvar.api.license	Gets the OakVar license information.
ov module info	oakvar.api.module.info	Gets information on a module.
ov module install	oakvar.api.module.install	Installs modules.
ov module installbase	oakvar.api.module.installbase	Installs system modules.
ov module ls	oakvar.api.module.ls	Lists modules.
ov module pack	oakvar.api.module.pack	Packs a module for registration at OakVar store.
ov module uninstall	oakvar.api.module.uninstall	Uninstalls modules.
ov module update	oakvar.api.module.update	Updates modules.
ov new exampleinput	oakvar.api.new.exampleinput	Creates an example input file.
ov new module	oakvar.api.new.module	Creates a template for a new module.
ov report	oakvar.api.report	Generates report files from OakVar result databases.
ov run	oakvar.api.run	Runs the OakVar annotation pipeline.
ov store delete	oakvar.api.store.delete	Deletes a module from the OakVar store.
ov store fetch	oakvar.api.store.fetch	Fetches the OakVar store cache.
ov store login	oakvar.api.store.login	Logs in to the OakVar store.
ov store logout	oakvar.api.store.logout	Logs out from the OakVar store.
ov store register	oakvar.api.store.register	Register a module at the OakVar store.
ov store url	oakvar.api.store.url	Gets the URL of the OakVar store.
ov store account change	oakvar.api.store.account.change	Changes the password of an OakVar store account.
ov store account check	oakvar.api.store.account.check	Checks if logged in at the OakVar store.
ov store account create	oakvar.api.store.account.create	Creats an OakVar store account.
ov store account delete	oakvar.api.store.account.delete	Deletes an OakVar store account.
ov store account reset	oakvar.api.store.account.reset	Invokes a password change email for an OakVar store account.
ov system account check	oakvar.api.system.check	Checks OakVar installation on the system.
ov system md	oakvar.api.system.md	Gets or sets the OakVar modules directory.
ov system setup	oakvar.api.system.setup	Sets up OakVar in the system.
ov update	oakvar.api.update	Gets OakVar version.
ov version	oakvar.api.version	Gets OakVar version.

OakVar Python API has a utility function to help data science with genomic data. If an OakVar analysis produced ov_result.sqlite result database file, the following will produce a Polars DataFrame from variant level data of the result database.

>>> import oakvar as ov
>>> df = ov.get_df_from_db("ov_result.sqlite", table="variant")