micom.qiime_formats#

Provides support for Qiime formats.

Module Contents#

Functions#

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.

Attributes#

yaml

_has_manifest

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.