mscompatibility

MSCompatibility()

This class compatibilizes a collection of individual metabolic models to facilitate syntrophy and accurate analysis of herefrom community models. This standardization leverages the ModelSEED Database as the arbitrator of metabolite and reaction IDs in the metabolic models:

from modelseedpy.community import MSCompatibility
ms_compat = MSCompatibility(modelseed_db_path, printing = True)

  • modelseed_db_path str: the path to the ModelSEED Database, which is only required for the FullThermo, where None does not apply these constraints.

  • printing bool: specifies whether results will be printed.

standardize()

Staticmethod

The IDs and names of the metabolites and reactions models are standardized to those of the ModelSEED Database:

new_models (, optionally unknown_met_ids) = MSCompatibility.standardize(models, metabolites=True, exchanges=True, conflicts_file_name=None, model_names=None,
                      export_directory=None, view_unknown_mets=True, printing=True, unknown_met_ids=None, changed_metabolites=None, changed_reactions=None)

  • models Iterable o cobra.core.model.Model: the collection of CobraKBase models that will be standardized. The conversion from standard COBRA models to CobraKBase models is facilitated by the cobrakbase package.

  • metabolites bool: specifies whether metabolites (True) or reactions (False) will be compared between the models.

  • exchanges bool: specifies whether only the exchanges of the models will be standardized.

  • conflicts_file_name str: the filename to where metabolite conflicts will be exported, where None does not export.

  • model_names list: the collection of model names that correspond with the indices of the models parameter, which is used to distinguish the exported files of each model.

  • export_directory str: specifies the directory to which all of the content will be exported.

  • view_unknown_mets & printing bool: specifies whether the unknown metabolite IDs and other results of the alignment functionality, respectively, are printed to the console for the user to review.

  • unknown_met_ids, changed_metabolites, & changed_reactions Iterable: collections of unknown metabolite IDs and corrected metabolites and reactions. These are internal entities that are passed as argumented to standardize() by align_exchanges() when the latter is provided True through the standardize parameter.

returns the collection of standardized COBRA models, and possibly the collection of unknown metabolite IDs

align_exchanges()

Staticmethod

The exchange reactions and metabolites of metabolic models are aligned to facilitate community assemblage and cross-feeding interactions:

new_models (, optionally extras) = MSCompatibility.align_exchanges(models, standardize=False, conflicts_file_name=None,
                                                   model_names=None, export_directory=None, printing=True, extras=False)

  • models Iterable o cobra.core.model.Model: the collection of CobraKBase models that will be standardized. The conversion from standard COBRA models to CobraKBase models is facilitated by the cobrakbase package.

  • standardize bool: specifies whether the models will be standardized through the standardize function.

  • conflicts_file_name str: the filename to where metabolite conflicts will be exported, where None does not export.

  • model_names Iterable: the collection of model names that correspond with the indices of the models parameter, which is used to distinguish the exported files of each model.

  • export_directory str: specifies the directory to which all of the content will be exported.

  • printing bool: specifies whether results of the alignment functionality, respectively, are printed to the console for the user to review.

  • extras bool: specifies whether the unique_mets, unknown_met_ids, changed_metabolites, and changed_reactions collections of internal data are provided in a tuple, respectively, as the second returned object from the function. This information is not provided, and the function returns one object, when this parameter is False.

returns the collection of aligned COBRA models, and possibly the collection of the aforementioned extras