micom.taxonomy#

Helpers to convert external data to a MICOM taxonomy.

Module Contents#

Functions#

build_from_qiime(→ pandas.DataFrame)

Build the specification for the community models.

qiime_to_micom(feature_table, taxonomy[, collapse_on])

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