lmpy.data_wrangling.tree.base

Module containing Tree Data Wrangler base class.

Module Contents

Classes

_TreeDataWrangler

Constructor for _TreeDataWrangler base class.
class lmpy.data_wrangling.tree.base._TreeDataWrangler(**params)[source]

Bases: lmpy.data_wrangling.base._DataWrangler

Constructor for _TreeDataWrangler base class.

Parameters

**params (dict) – Named parameters to pass to _DataWrangler base class.

name = _TreeDataWrangler[source]
_report_tip(self, modified=False, purged=False)[source]

Report what is done on a tree tip.

Parameters

  • modified (bool) – Was the tip modified.

  • purged (bool) – Was the tip purged.

get_report(self)[source]

Get the report of the wrangler’s activities.

Returns

Wrangler report information.

Return type

dict

abstract wrangle_tree(self, tree)[source]

Wrangle a tree.

Parameters

tree (TreeWrapper) – A phylogenetic tree to wrangle.

Raises

NotImplementedError – This method is not implemeneted for the base class.