ppanggolin.mod package

Submodules

ppanggolin.mod.module module

ppanggolin.mod.module.check_pangenome_former_modules(pangenome: Pangenome, force: bool = False)

Checks pangenome status and .h5 files for former modules, delete them if allowed or raise an error

Parameters:

  • pangenome – Pangenome object

  • force – Allow to force write on pangenome by erasing already present modules

ppanggolin.mod.module.compute_mod_graph(pangenome: Pangenome, t: int = 1, disable_bar: bool = False)

Computes a graph using all provided genomes with a transitive closure of size t

Parameters:

  • pangenome – pangenome with organisms to compute the graph

  • t – the size of the transitive closure

  • disable_bar – whether to show a progress bar or not

ppanggolin.mod.module.compute_modules(g: Graph, multi: set, weight: float = 0.85, min_fam: int = 2, size: int = 3)

Computes modules using a graph built by ppanggolin.mod.module.compute_mod_graph() and different parameters defining how restrictive the modules will be.

Parameters:
ppanggolin.mod.module.launch(args: Namespace)

Command launcher

Parameters:

args – All arguments provide by user

ppanggolin.mod.module.parser_module(parser: ArgumentParser)

Parser for specific argument of module command

Parameters:

parser – parser for align argument

ppanggolin.mod.module.predict_modules(pangenome: Pangenome, dup_margin: float = 0.05, size: int = 3, min_presence: int = 2, transitive: int = 4, jaccard: float = 0.85, force: bool = False, disable_bar: bool = False)

Main function to predict module

Parameters:

  • pangenome – Pangenome object with Gene Families, Annotation and Partition

  • dup_margin – minimum ratio of organisms in which family must have multiple genes to be considered duplicated

  • size – Minimal number of gene family in a module

  • min_presence – Minimum number of times the module needs to be present in the pangenome to be reported.

  • transitive – Size of the transitive closure used to build the graph.

  • jaccard – minimum jaccard similarity used to filter edges between gene families.

  • force – Allow to force write on Pangenome file

  • disable_bar – Disable progress bar

ppanggolin.mod.module.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