ppanggolin.meta package

Submodules

ppanggolin.meta.meta module

ppanggolin.meta.meta.assign_metadata(metadata_df: DataFrame, pangenome: Pangenome, source: str, metatype: str, omit: bool = False, disable_bar: bool = False)

function assigns metadata to elements in a pangenome based on a metadata dataframe. :param metadata_df: A pandas dataframe containing metadata to be assigned to elements in the pangenome. :param pangenome: A Pangenome object representing the pangenome to which metadata will be assigned. :param source: A string representing the source of the metadata. :param metatype: A string representing the type of element to which metadata will be assigned. :param omit: A boolean indicating whether to raise an error if metadata cannot be assigned to an element. If True, metadata will not be assigned to elements that do not exist in the pangenome. If False, an error will be raised. Default is False. :param disable_bar: A boolean indicating whether to disable the progress bar. Default is False.

Raises:

  • KeyError – element name is not find in pangenome

  • AssertionError – Metatype is not recognized

ppanggolin.meta.meta.check_metadata_arguments(args: Namespace, parser: ArgumentParser) → str

Check the arguments provided for and raise errors if they are incompatible or missing.

Parameters:

  • args – An argparse.Namespace object containing parsed command-line arguments.

  • parser – parser of the command

Returns:

A string indicating the input mode (‘single’ or ‘multiple’).

ppanggolin.meta.meta.check_metadata_format(metadata: Path, metatype: str) → DataFrame

Check if the TSV with metadata respect the input format

Parameters:

  • metadata – Path to the TSV file with metadata

  • metatype – Indicate which pangenome element metadata will be added

Returns:

Dataframe with metadata loaded

ppanggolin.meta.meta.check_pangenome_metadata(pangenome: Pangenome, source: str, metatype: str, force: bool = False, disable_bar: bool = False)

Check and load pangenome information before adding metadata

Parameters:

  • pangenome – Pangenome object

  • source – source of the metadata

  • metatype – select to which pangenome element metadata will be added

  • force – erase if a metadata for the provide source and metatype already exist

  • disable_bar – Disable bar

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

Command launcher

Parameters:

args – All arguments provide by user

ppanggolin.meta.meta.parser_meta(parser: ArgumentParser)

Parser for specific argument of graph command

Parameters:

parser – parser for align argument

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

Subparser to launch PPanGGOLiN in Command line

:param sub_parser : sub_parser for align command

:return : parser arguments for align command

Module contents