ppanggolin.metrics package

Submodules

ppanggolin.metrics.fluidity module

ppanggolin.metrics.fluidity.compute_genomes_fluidity(pangenome: Pangenome, disable_bar: bool = False) → dict

Compute the genomes’ fluidity from the pangenome

Parameters:

  • pangenome – pangenome which will be used to compute the genomes’ fluidity

  • disable_bar – Disable the progress bar

Returns:

Genomes fluidity value from the pangenome for each partition

ppanggolin.metrics.fluidity.fam_fluidity(pangenome: Pangenome, disable_bar: bool = False) → dict

Compute the family fluidity from the pangenome

Parameters:

  • pangenome – pangenome which will be used to compute the genomes’ fluidity

  • disable_bar – Disable the progress bar

Returns:

family fluidity value from the pangenome for each partition

ppanggolin.metrics.fluidity.nb_fam_per_org(pangenome: Pangenome, disable_bar: bool = False) → dict

Create a dictionary with for each organism the number of gene families

Parameters:

  • pangenome – Pangenome which contain the organisms and gene families

  • disable_bar – Disable the progress bar

Returns:

Dictionary with organisms as key and number of families as value

ppanggolin.metrics.fluidity.nb_org_per_fam(pangenome: Pangenome, disable_bar: bool = False) → dict

Create a dictionary with for each gene families the number of organism

Parameters:

  • pangenome – Pangenome which contain the organisms and gene families

  • disable_bar – Disable the progress bar

Returns:

Dictionary with organisms as key and number of families as value

ppanggolin.metrics.metrics module

ppanggolin.metrics.metrics.check_already_computed_metric(pangenome: Pangenome, genomes_fluidity: bool = False, print_metric: bool = True, recompute: bool = False)

Check if one of the asked metrics is not already computed

Parameters:

  • pangenome – pangenome object

  • genomes_fluidity – Ask to compute genome fluidity

  • print_metric – Print metrics if already computed

  • recompute – Are metrics going to be recompute

ppanggolin.metrics.metrics.compute_metrics(pangenome: Pangenome, genomes_fluidity: bool = False, families_fluidity: bool = False, disable_bar: bool = False) → dict

Compute the metrics

Parameters:

  • pangenome – pangenome which will be used to compute the genomes’ fluidity

  • genomes_fluidity – Ask to compute genome fluidity

  • families_fluidity – Ask to compute family fluidity

  • disable_bar – Disable the progress bar

Returns:

dictionary with all the metrics computed

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

Command launcher

Parameters:

args – All arguments provide by user

ppanggolin.metrics.metrics.parser_metrics(parser: ArgumentParser)

Argument parser for the ‘metrics’ command.

Parameters:

parser – Argument parser for the ‘metrics’ command.

ppanggolin.metrics.metrics.print_computed_metric(metrics_dict: dict)

Print metrics in yaml format

Params metrics_dict:

Dict of computed metrics

ppanggolin.metrics.metrics.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

ppanggolin.metrics.metrics.write_metrics(pangenome: Pangenome, metrics_dict: dict, print_metrics: bool = False)

Write the metrics computed in the pangenome

Parameters:

  • pangenome – pangenome which will be used to compute the genomes’ fluidity

  • metrics_dict – dictionary with all the metrics computed

  • print_metrics – enable print of metrics

Module contents