ppanggolin.graph package
Submodules
ppanggolin.graph.makeGraph module
- ppanggolin.graph.makeGraph.check_pangenome_for_neighbors_graph(pangenome, force, disable_bar=False)
Checks and read the pangenome for neighbors graph computing.
- Parameters:
pangenome – Pangenome object
force – Allow to force write on Pangenome file
disable_bar – Disable progress bar
- ppanggolin.graph.makeGraph.check_pangenome_former_graph(pangenome: Pangenome, force: bool = False)
Checks pangenome status and .h5 files for former neighbors graph, delete it if allowed or raise an error
- Parameters:
pangenome – Pangenome object
force – Allow to force write on Pangenome file
- ppanggolin.graph.makeGraph.compute_neighbors_graph(pangenome: Pangenome, remove_copy_number: int = 0, force: bool = False, disable_bar: bool = False)
Creates the Pangenome Graph. Will either load the information from the pangenome file if they are not loaded, or use the information loaded if they are.
- Parameters:
pangenome – Pangenome object
remove_copy_number – Maximum authorized repeat presence of gene families. if zero no remove
force – Allow to force write on Pangenome file
disable_bar – Disable progress bar
- ppanggolin.graph.makeGraph.launch(args: Namespace)
Command launcher
- Parameters:
args – All arguments provide by user
- ppanggolin.graph.makeGraph.parser_graph(parser: ArgumentParser)
Parser for specific argument of graph command
- Parameters:
parser – parser for graph argument
- ppanggolin.graph.makeGraph.remove_high_copy_number(pangenome, number)
Removes families present more than ‘number’ times from the pangenome graph
- Parameters:
pangenome – Pangenome object
number – Maximum authorized repeat presence
- ppanggolin.graph.makeGraph.subparser(sub_parser: _SubParsersAction) ArgumentParser
Subparser to launch PPanGGOLiN in Command line
:param sub_parser : sub_parser for graph command
:return : parser arguments for graph command