The graph package

This builds the pangenome graph, and eventually removes nodes from it.

Submodules

ppanggolin.graph.makeGraph module

ppanggolin.graph.makeGraph.checkPangenomeForNeighborsGraph(pangenome, force)[source]: Checks the pangenome for neighbors graph computing.

ppanggolin.graph.makeGraph.checkPangenomeFormerGraph(pangenome, force)[source]: checks pangenome status and .h5 files for former neighbors graph, delete it if allowed or raise an error

ppanggolin.graph.makeGraph.computeNeighborsGraph(pangenome, remove_copy_number=0, force=False)[source]: Creates the Pangenome Graph. Will either load the informations from the pangenome file if they are not loaded, or use the informations loaded if they are.

ppanggolin.graph.makeGraph.graphSubparser(subparser)[source]

ppanggolin.graph.makeGraph.launch(args)[source]

ppanggolin.graph.makeGraph.remove_high_copy_number(pangenome, number)[source]: removes families present more than ‘number’ times from the pangenome graph