Source code for cameo.core.utils

import six
import csv

from pandas import DataFrame


[docs]def get_reaction_for(model, value, add=True): """Get or create a reaction for a metabolite or a reaction. If value is a Metabolite or a Metabolite id, return any already existing demand or exchange reaction. If *add* is true, add a demand reaction if it does not already exist. Parameters ---------- model : cobra.Model The model to for which to get / create a reaction value: str, Reaction or Metabolite A reaction identifier, a Reaction or a Metabolite for which an exchange reaction is to be created. add: bool Adds a demand reaction for a metabolite if a metabolite is found for *value* Returns ------- Reaction Raises ------ KeyError If *value* does not match any Reaction or Metabolite """ try: reactions = model.reactions.get_by_any(value) except (ValueError, KeyError, TypeError): metabolite = model.metabolites.get_by_any(value)[0] reactions = model.reactions.query("^(EX|DM)_{}$".format(metabolite.id)) if len(reactions) == 0: if add: reactions = [model.add_boundary(metabolite, type='demand')] else: raise KeyError('Invalid target %s' % value) return reactions[0]
[docs]def medium(model): """Current medium for this model.""" reaction_ids = [] reaction_names = [] lower_bounds = [] upper_bounds = [] for ex in model.exchanges: metabolite = list(ex.metabolites.keys())[0] coeff = ex.metabolites[metabolite] if coeff * ex.lower_bound > 0: reaction_ids.append(ex.id) reaction_names.append(ex.name) lower_bounds.append(ex.lower_bound) upper_bounds.append(ex.upper_bound) return DataFrame({'reaction_id': reaction_ids, 'reaction_name': reaction_names, 'lower_bound': lower_bounds, 'upper_bound': upper_bounds}, index=None, columns=['reaction_id', 'reaction_name', 'lower_bound', 'upper_bound'])
[docs]def load_medium(model, medium_def, copy=False, delimiter="\t"): """ Loads a medium into the model. If copy is true it will return a copy of the model. Otherwise it applies the medium to itself. Supported formats TODO Parameters ---------- model : cobra.Model The model to load medium for medium_def: str, pandas.DataFrame, dict. The medium to load copy: boolean, optional If True copies the model, otherwise the changes will happen inplace. delimiter: str Only if loading the medium from a file. Returns ------- cobra.Model If copy=True, returns a copy of the model. """ if copy: model = model.copy() else: model = model if isinstance(medium_def, dict): _load_medium_from_dict(model, medium_def) elif isinstance(medium_def, DataFrame): _load_medium_from_dataframe(model, medium_def) elif isinstance(medium_def, six.string_types): _load_medium_from_file(model, medium_def, delimiter=delimiter) else: raise AssertionError("input type (%s) is not valid" % type(medium)) return model
def _load_medium_from_dict(model, medium_def): assert isinstance(medium_def, dict) for ex_reaction in model.exchanges: ex_reaction.lower_bound = medium_def.get(ex_reaction.id, 0) def _load_medium_from_file(model, file_path, delimiter="\t"): this_medium = {} with open(file_path, "rb") as csv_file: reader = csv.reader(csv_file, delimiter=delimiter) for row in reader: model.reactions.get_by_id(row[0]) this_medium[row[0]] = row[1] _load_medium_from_dict(model, this_medium) def _load_medium_from_dataframe(model, medium_df): assert isinstance(medium_df, DataFrame) for ex_reaction in model.exchanges: if ex_reaction.id in medium_df.reaction_id.values: medium_row = medium_df[medium_df.reaction_id == ex_reaction.id] ex_reaction.lower_bound = medium_row.lower_bound.values[0] else: ex_reaction.lower_bound = 0