predict_phenotype functions

get_functional_roles()

A function that determines the set of genome feature that match the parameterized ontological term:

roles = get_functional_roles(genome, ontology_term)

  • genome ModelSEED Genome: The ModelSEED Genome that will be classified.

  • ontology_term str: The ontological criteria that will assess the genome.

returns roles set: The set of genome features that match the parameterized ontological term.

get_list_functional_roles_from_kbase()

A function that determines the set of genome feature that match the parameterized ontological term:

roles = get_list_functional_roles_from_kbase(genome_ref, ws_client)

  • genome_ref str: The KBase genome reference that is used to extract content from a respective KBase workspace.

  • ws_client KBase object: The KBase client that is used to acquire the genome from the KBase workspace.

returns list_functional_roles list: The list of functional roles in the loaded genome.

extract_features_from_genome()

A function that assembles a unique list of features for the specified genome:

genome_features = genclass.extract_features_from_genome(genome, ontology_term)

  • genome ModelSEED Genome: The ModelSEED Genome that will be classified.

  • ontology_term str: The ontological criteria that will assess the genome.

returns genome_features dict: A list of genome features value with the key of "genome".

classify()

A function that predicts FBA solutions based upon a set of genome features and indicators:

media = genclass.classify(genome, ontology_term='RAST')

  • genome ModelSEED Genome: The ModelSEED Genome that will be classified.

  • ontology_term str: The ontological criteria that will assess the genome.

returns prediction str: The numerical prediction of the model based upon the set of genome features and indicators.