micom.taxonomy
==============

.. py:module:: micom.taxonomy

.. autoapi-nested-parse::

   Helpers to convert external data to a MICOM taxonomy.



Functions
---------

.. autoapisummary::

   micom.taxonomy.build_from_qiime
   micom.taxonomy.qiime_to_micom
   micom.taxonomy.rank_prefixes
   micom.taxonomy.unify_rank_prefixes
   micom.taxonomy.taxon_id


Module Contents
---------------

.. py:function:: build_from_qiime(abundance: pandas.DataFrame, taxonomy: pandas.Series, collapse_on: str = 'genus', trim_rank_prefix: bool = False) -> pandas.DataFrame

   Build the specification for the community models.


.. py:function:: qiime_to_micom(feature_table, taxonomy, collapse_on='genus')

   Load a micom taxonomy from Qiime 2 data.

   :param feature_table: Path to a Qiime 2 FeatureTable artifact.
   :type feature_table: str
   :param taxonomy: Path to a Qiime 2 FeatureData[Taxonomy] artifact.
   :type taxonomy: str
   :param collapse_on: The taxa ranks to collapse on. This will dictate how strict the database
                       matching will be as well.
   :type collapse_on: str or List[str]

   :returns: A micom taxonomy containing abundances and taxonomy calls in long
             format.
   :rtype: pd.DataFrame


.. py:function:: rank_prefixes(manifest: pandas.DataFrame) -> pandas.Series

   Get the used prefixes for taxonomic ranks.

   :param manifest: A model database manifest.
   :type manifest: pandas.DataFrame

   :returns: The detected prefix for each taxonomic rank in the manifest.
   :rtype: pandas.Series


.. py:function:: unify_rank_prefixes(taxonomy: pandas.DataFrame, manifest: pandas.DataFrame) -> pandas.DataFrame

   Handle taxonomic rank prefixes in the taxonomy or database manifest.

   :param taxonomy: A taxonomy table.
   :type taxonomy: pandas.DataFrame
   :param manifest: A database manifest.
   :type manifest: pandas.DataFrame

   :returns: The taxonomy with adjusted taxa names consistent with the database.
   :rtype: tuple of pandas.DataFrame


.. py:function:: taxon_id(term: str, rates: pandas.DataFrame) -> str

   Find the ID for a taxon.

   :param term: The search term.
   :type term: str
   :param rates: A table of growth rates.
   :type rates: pandas.Dataframe

   :returns: The ID of the found taxon. Will raise a ValueError if not found.
   :rtype: str