cobra.io.mat ============ .. py:module:: cobra.io.mat .. autoapi-nested-parse:: Provide functions for I/O in MATLAB (.mat) format. Attributes ---------- .. autoapisummary:: cobra.io.mat.scipy_sparse cobra.io.mat.logger cobra.io.mat.MET_MATLAB_TO_PROVIDERS cobra.io.mat.MET_PROVIDERS_TO_MATLAB cobra.io.mat.MET_NOTES_TO_MATLAB cobra.io.mat.MET_MATLAB_TO_NOTES cobra.io.mat.RXN_MATLAB_TO_PROVIDERS cobra.io.mat.RXN_PROVIDERS_TO_MATLAB cobra.io.mat.CONFIDENCE_STR cobra.io.mat.RXN_MATLAB_TO_NOTES cobra.io.mat.RXN_NOTES_TO_MATLAB cobra.io.mat.GENE_MATLAB_TO_PROVIDERS cobra.io.mat.GENE_PROVIDERS_TO_MATLAB cobra.io.mat.DICT_GENE cobra.io.mat.DICT_GENE_REV cobra.io.mat.DICT_MET cobra.io.mat.DICT_MET_REV cobra.io.mat.DICT_MET_NOTES cobra.io.mat.DICT_MET_NOTES_REV cobra.io.mat.DICT_REACTION cobra.io.mat.DICT_REACTION_REV cobra.io.mat.DICT_REACTION_NOTES cobra.io.mat.DICT_REACTION_NOTES_REV cobra.io.mat.DICT_REPLACE cobra.io.mat._bracket_re cobra.io.mat._underscore_re cobra.io.mat._pubmed_re cobra.io.mat._punctuation_re cobra.io.mat._double_punctuation_re cobra.io.mat._ec_re cobra.io.mat._chebi_re cobra.io.mat._sbo_re Functions --------- .. autoapisummary:: cobra.io.mat._get_id_compartment cobra.io.mat._cell cobra.io.mat._cell_to_str_list cobra.io.mat._cell_to_float_list cobra.io.mat.load_matlab_model cobra.io.mat.save_matlab_model cobra.io.mat.mat_parse_annotations cobra.io.mat.mat_parse_notes cobra.io.mat.annotations_to_mat cobra.io.mat.notes_to_mat cobra.io.mat.create_mat_dict cobra.io.mat.from_mat_struct Module Contents --------------- .. py:data:: scipy_sparse :value: None .. py:data:: logger .. py:data:: MET_MATLAB_TO_PROVIDERS .. py:data:: MET_PROVIDERS_TO_MATLAB .. py:data:: MET_NOTES_TO_MATLAB .. py:data:: MET_MATLAB_TO_NOTES .. py:data:: RXN_MATLAB_TO_PROVIDERS .. py:data:: RXN_PROVIDERS_TO_MATLAB .. py:data:: CONFIDENCE_STR :value: 'Confidence Level' .. py:data:: RXN_MATLAB_TO_NOTES .. py:data:: RXN_NOTES_TO_MATLAB .. py:data:: GENE_MATLAB_TO_PROVIDERS .. py:data:: GENE_PROVIDERS_TO_MATLAB .. py:data:: DICT_GENE :value: 'DICT_GENE' .. py:data:: DICT_GENE_REV :value: 'DICT_GENE_REV' .. py:data:: DICT_MET :value: 'DICT_MET' .. py:data:: DICT_MET_REV :value: 'DICT_MET_REV' .. py:data:: DICT_MET_NOTES :value: 'DICT_MET_NOTES' .. py:data:: DICT_MET_NOTES_REV :value: 'DICT_MET_NOTES_REV' .. py:data:: DICT_REACTION :value: 'DICT_REACTION' .. py:data:: DICT_REACTION_REV :value: 'DICT_REACTION_REV' .. py:data:: DICT_REACTION_NOTES :value: 'DICT_REACTION_NOTES' .. py:data:: DICT_REACTION_NOTES_REV :value: 'DICT_REACTION_NOTES_REV' .. py:data:: DICT_REPLACE :type: dict .. py:data:: _bracket_re .. py:data:: _underscore_re .. py:data:: _pubmed_re .. py:data:: _punctuation_re .. py:data:: _double_punctuation_re .. py:data:: _ec_re .. py:data:: _chebi_re .. py:data:: _sbo_re .. py:function:: _get_id_compartment(_id: str) -> str Extract the compartment from the `id` string. :param _id: The ID string to extract component from. :type _id: str :returns: The extracted component string. :rtype: str .. py:function:: _cell(x: Iterable[str]) -> numpy.ndarray Translate an iterable `x` into a MATLAB cell array. :param x: The data iterable to convert to cell array. :type x: iterable of str :returns: The converted cell array compatible with MATLAB. :rtype: numpy.ndarray .. py:function:: _cell_to_str_list(m_cell: numpy.ndarray, empty_value: Optional[str] = None, pattern_split: Optional[Pattern] = None, str_prefix: str = '') -> List Turn an ndarray (cell) to a list of strings. :param m_cell: :type m_cell: np.ndarray :param empty_value: What value to replace empty cells with. Default None. :type empty_value: str, optional :param pattern_split: Regular expression to use to split the expression. Used for annotations. Default None. :type pattern_split: Pattern, optional :param str_prefix: A prefix that will be added to each value in the list if present. Default "". :type str_prefix: str, optional :returns: A list of processed strings. :rtype: List .. py:function:: _cell_to_float_list(m_cell: numpy.ndarray, empty_value: Optional[float] = None, inf_value: Optional[float] = None) -> List Turn an ndarray (cell) to a list of floats. :param m_cell: :type m_cell: np.ndarray :param empty_value: What value to replace empty cells with. Default None. :type empty_value: float, optional :param inf_value: Replace infinite values with defined inf. Default None (don't replace), will be replaced by given value if given. :type inf_value: float, optional :returns: A list of processed floats. :rtype: List .. py:function:: load_matlab_model(infile_path: Union[str, pathlib.Path, IO], variable_name: Optional[str] = None, inf: float = np.inf) -> cobra.core.Model Load a cobra model stored as a .mat file. :param infile_path: File path or descriptor of the .mat file describing the cobra model. :type infile_path: str or Path or filehandle :param variable_name: The variable name of the model in the .mat file. If None, then the first MATLAB variable which looks like a COBRA model will be used (default None). :type variable_name: str, optional :param inf: The value to use for infinite bounds. Some solvers do not handle infinite values so for using those, set this to a high numeric value (default `numpy.inf`). :type inf: float, optional :returns: The cobra model as represented in the .mat file. :rtype: cobra.Model :raises ImportError: If scipy is not found in the Python environment. :raises IOError: If no COBRA model is found in the .mat file. .. py:function:: save_matlab_model(model: cobra.core.Model, file_name: Union[str, pathlib.Path, IO], varname: Optional[str] = None) -> None Save the cobra model as a .mat file. This .mat file can be used directly in cobratoolbox. :param model: The cobra model to represent. :type model: cobra.Model :param file_name: File path or descriptor that the MATLAB representation should be written to. :type file_name: str or file-like or Path :param varname: The name of the variable within the MATLAB workspace. Model ID is used if available, else 'exported_model' is used (default None). :type varname: str, optional .. py:function:: mat_parse_annotations(target_list: List[cobra.core.Object], mat_struct: numpy.ndarray, d_replace: str = DICT_MET) -> None Process mat structure annotations in place. Will process mat structured annotations and add them to a list of new entities (metabolites, reactions, genes) in a format based on identifiers.org. :param target_list: A list of cobra objects, including metabolites, reactions or genes. The annotations will be added to these lists. :type target_list: list[cobra.Object] :param mat_struct: A darray that includes the data imported from matlab file. :type mat_struct: np.ndarray :param d_replace: A string that points to the dictionary of converstions between MATLAB and providers. Default DICT_MET (for metabolite). :type d_replace: str .. py:function:: mat_parse_notes(target_list: List[cobra.core.Object], mat_struct: numpy.ndarray, d_replace: str = DICT_REACTION_NOTES) -> None Process mat structure notes in place. Will process mat structured notes and add them to a list of new entities (metabolites, reactions, genes) in a format based on identifiers.org. :param target_list: A list of cobra objects, including metabolites, reactions or genes. The notes will be added to these lists. :type target_list: list[cobra.Object] :param mat_struct: A darray that includes the data imported from matlab file. :type mat_struct: np.ndarray :param d_replace: A string that points to the dictionary of converstions between MATLAB and notes. Default DICT_REACTION_NOTES (for reactions). :type d_replace: str .. py:function:: annotations_to_mat(mat_dict: collections.OrderedDict, annotation_list: List[Dict], d_replace: str = DICT_MET_REV) -> None Process mat structure annotations in place. Will process mat structured annotations and add them to a list of new entities (metabolites, reactions, genes) in a format based on identifiers.org. :param mat_dict: An ordered dictionary having model attributes as keys and their respective values represented as arrays, as the values. Annotations will be inserted into this OrderdDict. :type mat_dict: OrderedDict :param annotation_list: A list of cobra annotations, in the form of a dictionary. :type annotation_list: list[Dict] :param d_replace: A string that points to the dictionary of converstions between MATLAB and providers. Default DICT_MET_REV (for metabolite). :type d_replace: str .. py:function:: notes_to_mat(mat_dict: collections.OrderedDict, note_list: List[Dict], d_replace: str = DICT_MET_REV) -> None Process mat structure notes in place. Will process mat structured annotations and add them to a list of new entities (metabolites, reactions, genes) in a format based on identifiers.org. :param mat_dict: An ordered dictionary having model attributes as keys and their respective values represented as arrays, as the values. Annotations will be inserted into this OrderdDict. :type mat_dict: OrderedDict :param note_list: A list of cobra annotations, in the form of a dictionary. :type note_list: list[Dict] :param d_replace: A string that points to the dictionary of converstions between MATLAB and providers. Default DICT_MET_REV (for metabolite). :type d_replace: str .. py:function:: create_mat_dict(model: cobra.core.Model) -> collections.OrderedDict Create a dictionary mapping model attributes to arrays. :param model: The model to create dictionary for. :type model: cobra.Model :returns: The ordered dictionary having model attributes as keys and their respective values represented as arrays, as the values. :rtype: OrderedDict .. py:function:: from_mat_struct(mat_struct: numpy.ndarray, model_id: Optional[str] = None, inf: float = np.inf) -> cobra.core.Model Create a model from the cobratoolbox struct. :param mat_struct: The `numpy.ndarray` that most likely contains the model, being chosen by load_matlab_file after loading the matlab structure via scipy_io.loadmat. :type mat_struct: numpy.ndarray :param model_id: The ID of the model generated. If None, will try to look for ID in model's description. If multiple IDs are found, the first one is used. If no IDs are found, will use 'imported_model' (default None). :type model_id: str, optional :param inf: The value to use for infinite bounds. Some solvers do not handle infinite values so for using those, set this to a high numeric value (default `numpy.inf`). :type inf: float, optional :returns: The model as represented in .mat file. :rtype: cobra.Model