micom.qiime_formats

Provides support for Qiime formats.

Attributes

Functions

load_pickle(filename)

Load a community model from a pickled version.

metadata(artifact)

Read metadata from a Qiime 2 artifact.

load_qiime_model_db(artifact, extract_path)

Prepare a model database for use.

load_qiime_manifest(artifact)

Prepare community models for use.

load_qiime_model(artifact, id)

Load a model from a Qiime 2 artifact.

load_qiime_medium(artifact)

Load a growth medium/diet from a Qiime 2 artifact.

load_qiime_feature_table(artifact)

Load a feature table from a Qiime 2 artifact.

load_qiime_taxonomy(artifact)

Load taxonomy feature data from a Qiime 2 artifact.

Module Contents

micom.qiime_formats.load_pickle(filename)[source]

Load a community model from a pickled version.

Parameters:

filename (str) – The file the community is stored in.

Returns:

The loaded community model.

Return type:

micom.Community

micom.qiime_formats.yaml[source]
micom.qiime_formats._has_manifest = ['CommunityModels[Pickle]', 'MetabolicModels[JSON]', 'MetabolicModels[SBML]'][source]
micom.qiime_formats.metadata(artifact)[source]

Read metadata from a Qiime 2 artifact.

micom.qiime_formats.load_qiime_model_db(artifact, extract_path)[source]

Prepare a model database for use.

micom.qiime_formats.load_qiime_manifest(artifact)[source]

Prepare community models for use.

micom.qiime_formats.load_qiime_model(artifact, id)[source]

Load a model from a Qiime 2 artifact.

micom.qiime_formats.load_qiime_medium(artifact)[source]

Load a growth medium/diet from a Qiime 2 artifact.

micom.qiime_formats.load_qiime_feature_table(artifact)[source]

Load a feature table from a Qiime 2 artifact.

micom.qiime_formats.load_qiime_taxonomy(artifact)[source]

Load taxonomy feature data from a Qiime 2 artifact.