micom.taxonomy

Helpers to convert external data to a MICOM taxonomy.

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.

rank_prefixes(→ pandas.Series)

Get the used prefixes for taxonomic ranks.

unify_rank_prefixes(→ pandas.DataFrame)

Handle taxonomic rank prefixes in the taxonomy or database manifest.

taxon_id(→ str)

Find the ID for a taxon.

Module Contents

micom.taxonomy.build_from_qiime(abundance: pandas.DataFrame, taxonomy: pandas.Series, collapse_on: str = 'genus', trim_rank_prefix: bool = False) → 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

micom.taxonomy.rank_prefixes(manifest: pandas.DataFrame) → pandas.Series[source]

Get the used prefixes for taxonomic ranks.

Parameters:

manifest (pandas.DataFrame) – A model database manifest.

Returns:

The detected prefix for each taxonomic rank in the manifest.

Return type:

pandas.Series

micom.taxonomy.unify_rank_prefixes(taxonomy: pandas.DataFrame, manifest: pandas.DataFrame) → pandas.DataFrame[source]

Handle taxonomic rank prefixes in the taxonomy or database manifest.

Parameters:

  • taxonomy (pandas.DataFrame) – A taxonomy table.

  • manifest (pandas.DataFrame) – A database manifest.

Returns:

The taxonomy with adjusted taxa names consistent with the database.

Return type:

tuple of pandas.DataFrame

micom.taxonomy.taxon_id(term: str, rates: pandas.DataFrame) → str[source]

Find the ID for a taxon.

Parameters:

  • term (str) – The search term.

  • rates (pandas.Dataframe) – A table of growth rates.

Returns:

The ID of the found taxon. Will raise a ValueError if not found.

Return type:

str