micom.taxonomy
#
Helpers to convert external data to a MICOM taxonomy.
Module Contents#
Functions#
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Build the specification for the community models. |
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Load a micom taxonomy from Qiime 2 data. |
- micom.taxonomy.build_from_qiime(abundance, taxonomy: pandas.Series, collapse_on='genus') pandas.DataFrame [source]#
Build the specification for the community models.
- micom.taxonomy.qiime_to_micom(feature_table, taxonomy, collapse_on='genus')[source]#
Load a micom taxonomy from Qiime 2 data.
- Parameters:
feature_table (str) – Path to a Qiime 2 FeatureTable artifact.
taxonomy (str) – Path to a Qiime 2 FeatureData[Taxonomy] artifact.
collapse_on (str or List[str]) – The taxa ranks to collapse on. This will dictate how strict the database matching will be as well.
- Returns:
A micom taxonomy containing abundances and taxonomy calls in long format.
- Return type:
pd.DataFrame