ppanggolin.workflow package

Submodules

ppanggolin.workflow.all module

ppanggolin.workflow.all.add_workflow_args(parser: ArgumentParser)

Parser for important arguments that can be changed in CLI. Other (less important) arguments that are step specific can be changed in the config file. :param parser: parser for workflow argument

ppanggolin.workflow.all.check_translation_table(args)

Check translation table consistency in workflow context.

ppanggolin.workflow.all.launch(args: Namespace)

Command launcher

Parameters:

args – All arguments provide by user

ppanggolin.workflow.all.launch_workflow(args: Namespace, panrgp: bool = True, panmodule: bool = True)

Unified function to launch ppanggolin workflow.

Parameters:

• args – All arguments provide by command line

• panrgp – Flag to launch RGP prediction

• panmodule – Flag to launch module prediction

ppanggolin.workflow.all.subparser(sub_parser: _SubParsersAction) → ArgumentParser

Subparser to launch PPanGGOLiN in Command line :param sub_parser : sub_parser for all command :return : parser arguments for all command

ppanggolin.workflow.panModule module

ppanggolin.workflow.panModule.launch(args: Namespace)

Command launcher

Parameters:

args – All arguments provide by user

ppanggolin.workflow.panModule.subparser(sub_parser: _SubParsersAction) → ArgumentParser

Subparser to launch PPanGGOLiN in Command line :param sub_parser : sub_parser for all command :return : parser arguments for all command

ppanggolin.workflow.panRGP module

ppanggolin.workflow.panRGP.launch(args: Namespace)

Command launcher

Parameters:

args – All arguments provide by user

ppanggolin.workflow.panRGP.subparser(sub_parser: _SubParsersAction) → ArgumentParser

Subparser to launch PPanGGOLiN in Command line :param sub_parser : sub_parser for all command :return : parser arguments for all command

ppanggolin.workflow.workflow module

ppanggolin.workflow.workflow.launch(args: Namespace)

Command launcher

Parameters:

args – All arguments provide by user

ppanggolin.workflow.workflow.subparser(sub_parser: _SubParsersAction) → ArgumentParser

Subparser to launch PPanGGOLiN in Command line :param sub_parser : sub_parser for all command :return : parser arguments for all command

Module contents