biotaphy.data_wrangling.matrix.accepted_name_data_wrangler

Module containing accepted name wrangler for a matrix using Open Tree of Life.

Module Contents

Classes

BiotaphyAcceptedNameMatrixWrangler

Constructor for AcceptedNameMatrixModifier class.
class biotaphy.data_wrangling.matrix.accepted_name_data_wrangler.BiotaphyAcceptedNameMatrixWrangler(name_map=None, name_resolver=None, taxon_axis=1, purge_failures=True, out_map_filename=None, map_write_interval=100, out_map_format='json', **params)[source]

Bases: lmpy.data_wrangling.matrix.accepted_name_wrangler.AcceptedNameMatrixWrangler

Constructor for AcceptedNameMatrixModifier class.

Parameters

  • name_map (dict) – A map of original name to accepted name.

  • name_resolver (str or Method) – If provided, use this method for getting new accepted names. If set to ‘gbif’, use GBIF name resolution.

  • taxon_axis (int) – The axis with taxon headers.

  • purge_failures (bool) – Should failures be purged from the matrix.

  • out_map_filename (str) – A file location to write the updated name map.

  • map_write_interval (int) – Update the name map output file after each set of this many iterations.

  • out_map_format (str) – The format to write the names map (csv or json).

  • **params (dict) – Keyword parameters to pass to _MatrixDataWrangler.

name = BiotaphyAcceptedNameMatrixWrangler[source]
version = 1.0[source]