Functional Similarity (FS)

fs()

The Jiccard Index between two organism’s genomes is determined to assess their functional similarity:

CommScores.fs(models:Iterable=None, kbase_object=None, cobrakbase_repo_path:str=None,
              kbase_token_path:str=None, annotated_genomes:dict=None, printing=False)

• models list|set: The models from which pairwise combinations will be created and then evaluated.

• kbase_object cobrakbase.kbaseapi.KBaseAPI: The KBase API object that allows the corresponding genomes for each model to acquired.

• cobrakbase_repo_path str: The path to the COBRA-KBase GitHub repository, from which a kbase_object object will be created where it is not provided and where the genomes are not explicitly given by annotated_genomes.

• kbase_token_path str: The path to a kbase user token, which is necessary to access and acquire content from KBase.

• annotated_genomes dict: The collection of annotated genomes that will be compared, as an alternative to acquiring the model genomes via kbase_object.

• printing bool: specifies whether progress and auxillary information is printed during the anaysis.

Returns dict: The FS score, as the Jiccard Index of the gene ontologies between each member’s genome, with keys of the two member’s genome IDs delimited by ” ++ “.