def _data_frame(solution):
notice("%s: %f" % self.solutions.axes[0][solution - 1][0])
notice("%s: %f" % self.solutions.axes[0][solution - 1][1])
df = self.solutions.iloc[solution - 1]
df = df[abs(df.normalized_gaps) >= non_zero_flux_threshold]
df = df.sort_values('normalized_gaps')
display(df)
def _data_frame(solution):
df = self.nth_panel(solution - 1)
notice("biomass: {0:g}".format(df['biomass'].iat[0]))
notice("production: {0:g}".format(df['production'].iat[0]))
df = df.loc[abs(df['normalized_gaps']) >= non_zero_flux_threshold]
df.sort_values('normalized_gaps', inplace=True)
display(df)
def _data_frame(solution):
df = self.nth_panel(solution - 1)
notice("biomass: {0:g}".format(df['biomass'].iat[0]))
notice("production: {0:g}".format(df['production'].iat[0]))
df = df.loc[abs(df['normalized_gaps']) >= non_zero_flux_threshold]
df.sort_values('normalized_gaps', inplace=True)
display(df)
def plot(self, grid=None, width=None, height=None, title=None, axis_font_size=None):
if len(self.variable_ids) > 1:
notice("Multi-dimensional plotting is not supported")
return
plotting.plot_production_envelope(self._phase_plane, objective=self.objective, key=self.variable_ids[0],
grid=grid, width=width, height=height, title=title,
axis_font_size=axis_font_size)
def __call__(self, product='L-glutamate', hosts=hosts, database=None, view=config.default_view):
"""The works.
The following workflow will be followed to determine suitable
metabolic engineering strategies for a desired product:
- Determine production pathways for desired product and host organisms.
Try a list of default hosts if no hosts are specified.
- Determine maximum theoretical yields and production envelopes for
all routes.
- Determine if production routes can be coupled to growth.
- Determine over-expression, down-regulation, and KO targets.
Parameters
----------
product : str or Metabolite
The desired product.
hosts : list or Model or Host
A list of hosts (e.g. cameo.api.hosts), models, mixture thereof, or a single model or host.
Returns
-------
Designs
"""
if database is None:
database = universal.metanetx_universal_model_bigg_rhea
notice("Starting searching for compound %s" % product)
product = self.__translate_product_to_universal_reactions_model_metabolite(product, database)
pathways = self.predict_pathways(product, hosts=hosts, database=database)
optimization_reports = self.optimize_strains(pathways, view)
return optimization_reports
def predict_pathways(self, product, hosts=None, database=None): # TODO: make this work with a single host or model
"""Predict production routes for a desired product and host spectrum.
Parameters
----------
product : str or Metabolite
The desired product.
hosts : list or Model or Host
A list of hosts (e.g. cameo.api.hosts), models, mixture thereof, or a single model or host.
Returns
-------
dict
...
"""
pathways = dict()
product = self.__translate_product_to_universal_reactions_model_metabolite(product, database)
for host in hosts:
logging.debug('Processing host {}'.format(host.name))
if isinstance(host, Model):
host = Host(name='UNKNOWN_HOST', models=[host])
for model in list(host.models):
identifier = searching()
logging.debug('Processing model {} for host {}'.format(model.id, host.name))
notice('Predicting pathways for product %s in %s (using model %s).'
% (product.name, host, model.id))
logging.debug('Predicting pathways for model {}'.format(model.id))
pathway_predictor = pathway_prediction.PathwayPredictor(model,
universal_model=database,
compartment_regexp=re.compile(".*_c$"))
# TODO adjust these numbers to something reasonable
predicted_pathways = pathway_predictor.run(product, max_predictions=4, timeout=3 * 60, silent=True)
stop_loader(identifier)
pathways[(host, model)] = predicted_pathways
self.__display_pathways_information(predicted_pathways, host, model)
return pathways
def plot(self, index=None, variables=None, grid=None, width=None, height=None, title=None, palette=None, **kwargs):
if len(self.variable_ids) > 1:
notice("Multi-dimensional plotting is not supported")
return
if index is not None:
self._plot_flux_variability_analysis(index, variables=variables, width=width, grid=grid, palette=palette)
else:
self._plot_production_envelope(title=title, grid=grid, width=width, height=height)
def plot(self, grid=None, width=None, height=None, title=None):
if len(self.variable_ids) > 1:
notice("Multi-dimensional plotting is not supported")
return
title = "DifferentialFVA Result" if title is None else title
x = [elem[0][1] for elem in list(self.solutions.items)]
y = [elem[1][1] for elem in list(self.solutions.items)]
colors = ["red" for _ in x]
plotting.plot_production_envelope(self._phase_plane, objective=self.objective, key=self.variable_ids[0],
grid=grid, width=width, height=height, title=title,
points=[x, y], points_colors=colors)
def __translate_product_to_universal_reactions_model_metabolite(self, product, database):
if isinstance(product, Metabolite):
return product
elif isinstance(product, str):
search_result = products.search(product)
notice("Found %d compounds that match query '%s'" % (len(search_result), product))
self.__display_product_search_result(search_result)
notice("Choosing best match (%s) ... please interrupt if this is not the desired compound."
% search_result.name[0])
self.__display_compound(search_result.InChI[0])
return database.metabolites.get_by_id(search_result.index[0])
def translate_product_to_universal_reactions_model_metabolite(self, product, database):
if isinstance(product, Metabolite):
return product
elif isinstance(product, six.text_type) or isinstance(product, six.string_types):
search_result = products.search(product)
search_result = search_result.loc[[i for i in search_result.index if i in database.metabolites]]
if len(search_result) == 0:
raise KeyError("No compound matches found for query %s" % product)
notice("Found %d compounds that match query '%s'" % (len(search_result), product))
self.__display_product_search_result(search_result)
notice("Choosing best match (%s) ... please interrupt if this is not the desired compound."
% search_result.name.values[0])
self.__display_compound(search_result.InChI.values[0])
return database.metabolites.get_by_id(search_result.index[0])
def translate_product_to_universal_reactions_model_metabolite(self, product, database):
if isinstance(product, Metabolite):
return product
elif isinstance(product, six.text_type) or isinstance(product, six.string_types):
search_result = products.search(product)
search_result = search_result.loc[[i for i in search_result.index if i in database.metabolites]]
if len(search_result) == 0:
raise KeyError("No compound matches found for query %s" % product)
notice("Found %d compounds that match query '%s'" % (len(search_result), product))
self.__display_product_search_result(search_result)
notice("Choosing best match (%s) ... please interrupt if this is not the desired compound."
% search_result.name.values[0])
self.__display_compound(search_result.InChI.values[0])
return database.metabolites.get_by_id(search_result.index[0])
def __translate_product_to_universal_reactions_model_metabolite(
self, product, database):
if isinstance(product, Metabolite):
return product
elif isinstance(product, str):
search_result = products.search(product)
notice("Found %d compounds that match query '%s'" %
(len(search_result), product))
self.__display_product_search_result(search_result)
notice(
"Choosing best match (%s) ... please interrupt if this is not the desired compound."
% search_result.name[0])
self.__display_compound(search_result.InChI[0])
return database.metabolites.get_by_id(search_result.index[0])
def predict_pathways(self, product, hosts, database, aerobic=True):
"""Predict production routes for a desired product and host spectrum.
Parameters
----------
product : str or Metabolite
The desired product.
hosts : list
A list of hosts (e.g. cameo.api.hosts), models, mixture thereof, or a single model or host.
database: Model
A model to use as database. See also: cameo.models.universal
aerobic: bool
If True, it will set `model.reactions.EX_o2_e.lower_bound` to 0.
Returns
-------
dict
([Host, Model] -> PredictedPathways)
"""
pathways = dict()
product = self.__translate_product_to_universal_reactions_model_metabolite(
product, database)
for host in hosts:
logging.debug('Processing host {}'.format(host.name))
if isinstance(host, Model):
host = Host(name='UNKNOWN_HOST', models=[host])
for model in list(host.models):
with model:
if not aerobic and "EX_o2_e" in model.reactions:
model.reactions.EX_o2_e.lower_bound = 0
identifier = searching()
logging.debug('Processing model {} for host {}'.format(
model.id, host.name))
notice(
'Predicting pathways for product %s in %s (using model %s).'
% (product.name, host, model.id))
logging.debug('Predicting pathways for model {}'.format(
model.id))
pathway_predictor = pathway_prediction.PathwayPredictor(
model, universal_model=database)
predicted_pathways = pathway_predictor.run(
product,
max_predictions=self.options.max_pathway_predictions,
timeout=self.options.pathway_prediction_timeout,
silent=not self.options.verbose)
stop_loader(identifier)
pathways[(host, model)] = predicted_pathways
self.__display_pathways_information(
predicted_pathways, host, model)
return pathways
def __call__(self,
product='L-glutamate',
hosts=HOSTS,
database=None,
aerobic=True,
view=config.default_view):
"""The works.
The following workflow will be followed to determine suitable
metabolic engineering strategies for a desired product:
- Determine production pathways for desired product and host organisms.
Try a list of default hosts if no hosts are specified.
- Determine maximum theoretical yields and production envelopes for
all routes.
- Determine if production routes can be coupled to growth.
- Determine over-expression, down-regulation, and KO targets.
Parameters
----------
product : str or Metabolite
The desired product.
hosts : list or Model or Host
A list of hosts (e.g. cameo.api.hosts), models, mixture thereof, or a single model or host.
aerobic: bool
If false, sets `model.reaction.EX_o2_e.lower_bound = 0`
Returns
-------
Designs
"""
if database is None:
database = universal.metanetx_universal_model_bigg
notice("Starting searching for compound %s" % product)
try:
product = self.__translate_product_to_universal_reactions_model_metabolite(
product, database)
except Exception:
raise KeyError("Product %s is not in the %s database" %
(product, database.id))
pathways = self.predict_pathways(product,
hosts=hosts,
database=database,
aerobic=aerobic)
optimization_reports = self.optimize_strains(pathways,
view,
aerobic=aerobic)
return optimization_reports
def predict_pathways(
self,
product,
hosts=None,
database=None): # TODO: make this work with a single host or model
"""Predict production routes for a desired product and host spectrum.
Parameters
----------
product : str or Metabolite
The desired product.
hosts : list or Model or Host
A list of hosts (e.g. cameo.api.hosts), models, mixture thereof, or a single model or host.
Returns
-------
dict
...
"""
pathways = dict()
product = self.__translate_product_to_universal_reactions_model_metabolite(
product, database)
for host in hosts:
logging.debug('Processing host {}'.format(host.name))
if isinstance(host, Model):
host = Host(name='UNKNOWN_HOST', models=[host])
for model in list(host.models):
identifier = searching()
logging.debug('Processing model {} for host {}'.format(
model.id, host.name))
notice(
'Predicting pathways for product %s in %s (using model %s).'
% (product.name, host, model.id))
logging.debug('Predicting pathways for model {}'.format(
model.id))
pathway_predictor = pathway_prediction.PathwayPredictor(
model,
universal_model=database,
compartment_regexp=re.compile(".*_c$"))
# TODO adjust these numbers to something reasonable
predicted_pathways = pathway_predictor.run(product,
max_predictions=4,
timeout=3 * 60,
silent=True)
stop_loader(identifier)
pathways[(host, model)] = predicted_pathways
self.__display_pathways_information(predicted_pathways, host,
model)
return pathways
def plot(self,
grid=None,
width=None,
height=None,
title=None,
axis_font_size=None):
if len(self.variable_ids) > 1:
notice("Multi-dimensional plotting is not supported")
return
plotting.plot_production_envelope(self._phase_plane,
objective=self.objective,
key=self.variable_ids[0],
grid=grid,
width=width,
height=height,
title=title,
axis_font_size=axis_font_size)
def plot(self, grid=None, width=None, height=None, title=None):
if len(self.variable_ids) > 1:
notice("Multi-dimensional plotting is not supported")
return
title = "DifferentialFVA Result" if title is None else title
x = [elem[0][1] for elem in list(self.solutions.items)]
y = [elem[1][1] for elem in list(self.solutions.items)]
colors = ["red" for _ in x]
plotting.plot_production_envelope(self._phase_plane,
objective=self.objective,
key=self.variable_ids[0],
grid=grid,
width=width,
height=height,
title=title,
points=[x, y],
points_colors=colors)
def plot(self, grid=None, width=None, height=None, title=None, axis_font_size=None, palette=None,
points=None, points_colors=None, **kwargs):
if title is None:
title = "Phenotypic Phase Plane"
if len(self.variable_ids) == 1:
variable = self.variable_ids[0]
x_axis_label = self.nice_variable_ids[0]
y_axis_label = self.nice_objective_id
dataframe = pandas.DataFrame(columns=["ub", "lb", "value", "strain"])
for _, row in self.iterrows():
_df = pandas.DataFrame([[row['objective_upper_bound'], row['objective_lower_bound'], row[variable], "WT"]],
columns=dataframe.columns)
dataframe = dataframe.append(_df)
plot = plotter.production_envelope(dataframe, grid=grid, width=width, height=height,
title=title, y_axis_label=y_axis_label, x_axis_label=x_axis_label,
palette=palette, points=points, points_colors=points_colors)
elif len(self.variable_ids) == 2:
var_1 = self.variable_ids[0]
var_2 = self.variable_ids[1]
x_axis_label = self.nice_variable_ids[0]
y_axis_label = self.nice_variable_ids[1]
z_axis_label = self.nice_objective_id
dataframe = pandas.DataFrame(columns=["ub", "lb", "value1", "value2", "strain"])
for _, row in self.iterrows():
_df = pandas.DataFrame([[row['objective_upper_bound'], row['objective_lower_bound'],
row[var_1], row[var_2], "WT"]],
columns=dataframe.columns)
dataframe = dataframe.append(_df)
plot = plotter.production_envelope_3d(dataframe, grid=grid, width=width, height=height,
title=title, y_axis_label=y_axis_label, x_axis_label=x_axis_label,
z_axis_label=z_axis_label, palette=palette, points=points,
points_colors=points_colors)
else:
notice("Multi-dimensional plotting is not supported")
return
if grid is None:
plotter.display(plot)
def predict_pathways(self, product, hosts, database, aerobic=True):
"""Predict production routes for a desired product and host spectrum.
Parameters
----------
product : str or Metabolite
The desired product.
hosts : list
A list of hosts (e.g. cameo.api.hosts), models, mixture thereof, or a single model or host.
database: Model
A model to use as database. See also: cameo.models.universal
aerobic: bool
If True, it will set `model.reactions.EX_o2_e.lower_bound` to 0.
Returns
-------
dict
([Host, Model] -> PredictedPathways)
"""
pathways = dict()
product = self.translate_product_to_universal_reactions_model_metabolite(product, database)
for host in hosts:
logging.debug('Processing host {}'.format(host.name))
if isinstance(host, Model):
host = Host(name='UNKNOWN_HOST', models=[host])
for model in list(host.models):
with model:
if not aerobic and "EX_o2_e" in model.reactions:
model.reactions.EX_o2_e.lower_bound = 0
identifier = searching()
logging.debug('Processing model {} for host {}'.format(model.id, host.name))
notice('Predicting pathways for product %s in %s (using model %s).'
% (product.name, host, model.id))
logging.debug('Predicting pathways for model {}'.format(model.id))
pathway_predictor = pathway_prediction.PathwayPredictor(model, universal_model=database)
predicted_pathways = pathway_predictor.run(product,
max_predictions=self.options.max_pathway_predictions,
timeout=self.options.pathway_prediction_timeout,
silent=not self.options.verbose)
stop_loader(identifier)
pathways[(host, model)] = predicted_pathways
self.__display_pathways_information(predicted_pathways, host, model)
return pathways
def plot(self,
grid=None,
width=None,
height=None,
title=None,
axis_font_size=None,
palette=None,
points=None,
points_colors=None,
estimate='flux',
**kwargs):
"""plot phenotypic phase plane result
create a plot of a phenotypic phase plane analysis
Parameters
----------
grid: plotting grid
the grid for plotting
width: int
the width of the plot
height: int
the height of the plot
title: string
the height of the plot
axis_font_size: int
the font sizes for the axis
palette: string
name of color palette to use, e.g. RdYlBlu
points: iterable of points
additional points to plot as x, y iterable
points_colors: iterable of strings
iterable with colors for the points
estimate: string
either flux, mass_yield (g output / g output) or c_yield (mol carbon output / mol carbon input)
"""
possible_estimates = {
'flux': ('objective_upper_bound', 'objective_lower_bound', 'flux',
'[mmol gDW^-1 h^-1]'),
'mass_yield': ('mass_yield_upper_bound', 'mass_yield_lower_bound',
'mass yield, src={}'.format(self.source_reaction),
'[g/g(src) h^-1]'),
'c_yield': ('c_yield_upper_bound', 'c_yield_lower_bound',
'carbon yield, src={}'.format(self.source_reaction),
'[mmol(C)/mmol(C(src)) h^-1]')
}
if estimate not in possible_estimates:
raise Exception('estimate must be one of %s' %
', '.join(possible_estimates.keys()))
upper, lower, description, unit = possible_estimates[estimate]
if title is None:
title = "Phenotypic Phase Plane ({})".format(description)
if len(self.variable_ids) == 1:
variable = self.variable_ids[0]
y_axis_label = self._axis_label(self.objective,
self.nice_objective_id, unit)
x_axis_label = self._axis_label(variable,
self.nice_variable_ids[0],
'[mmol gDW^-1 h^-1]')
dataframe = pandas.DataFrame(
columns=["ub", "lb", "value", "strain"])
for _, row in self.iterrows():
_df = pandas.DataFrame(
[[row[upper], row[lower], row[variable], "WT"]],
columns=dataframe.columns)
dataframe = dataframe.append(_df)
plot = plotter.production_envelope(dataframe,
grid=grid,
width=width,
height=height,
title=title,
y_axis_label=y_axis_label,
x_axis_label=x_axis_label,
palette=palette,
points=points,
points_colors=points_colors)
elif len(self.variable_ids) == 2:
var_1 = self.variable_ids[0]
var_2 = self.variable_ids[1]
x_axis_label = self._axis_label(var_1, self.nice_variable_ids[0],
'[mmol gDW^-1 h^-1]')
y_axis_label = self._axis_label(var_2, self.nice_variable_ids[1],
'[mmol gDW^-1 h^-1]')
z_axis_label = self._axis_label(self.objective,
self.nice_objective_id, unit)
dataframe = pandas.DataFrame(
columns=["ub", "lb", "value1", "value2", "strain"])
for _, row in self.iterrows():
_df = pandas.DataFrame(
[[row[upper], row[lower], row[var_1], row[var_2], "WT"]],
columns=dataframe.columns)
dataframe = dataframe.append(_df)
plot = plotter.production_envelope_3d(dataframe,
grid=grid,
width=width,
height=height,
title=title,
y_axis_label=y_axis_label,
x_axis_label=x_axis_label,
z_axis_label=z_axis_label,
palette=palette,
points=points,
points_colors=points_colors)
else:
notice("Multi-dimensional plotting is not supported")
return
if grid is None:
plotter.display(plot)
def _data_frame(solution):
notice("%s: %f" % self.solutions.axes[0][solution - 1][0])
notice("%s: %f" % self.solutions.axes[0][solution - 1][1])
display(self.solutions.iloc[solution - 1])
def display_pathway(pathway, i):
notice("Pathway %i" % i)
if in_ipnb():
display(pathway.data_frame)
else:
print(pathway.data_frame)
def display_pathway(pathway, i):
notice("Pathway %i" % i)
if in_ipnb():
display(pathway.data_frame)
else:
print(pathway.data_frame)
def predict_pathways(self,
product,
hosts=None,
database=None,
aerobic=True):
"""Predict production routes for a desired product and host spectrum.
Parameters
----------
product : str or Metabolite
The desired product.
hosts : list or Model or Host
A list of hosts (e.g. cameo.api.hosts), models, mixture thereof, or a single model or host.
database: SolverBasedModel
A model to use as database. See also: cameo.models.universal
aerobic: bool
If True, it will set `model.reactions.EX_o2_e.lower_bound` to 0.
Returns
-------
dict
([Host, Model] -> PredictedPathways)
"""
max_predictions = 8
timeout = 3 * 60
pathways = dict()
product = self.__translate_product_to_universal_reactions_model_metabolite(
product, database)
for host in hosts:
logging.debug('Processing host {}'.format(host.name))
if isinstance(host, Model):
host = Host(name='UNKNOWN_HOST', models=[host])
for model in list(host.models):
with TimeMachine() as tm:
if not aerobic and "EX_o2_e" in model.reactions:
model.reactions.EX_o2_e.change_bounds(lb=0,
time_machin=tm)
identifier = searching()
logging.debug('Processing model {} for host {}'.format(
model.id, host.name))
notice(
'Predicting pathways for product %s in %s (using model %s).'
% (product.name, host, model.id))
logging.debug('Predicting pathways for model {}'.format(
model.id))
pathway_predictor = pathway_prediction.PathwayPredictor(
model,
universal_model=database,
compartment_regexp=re.compile(".*_c$"))
if self.debug:
max_predictions = 2
timeout = 60
predicted_pathways = pathway_predictor.run(
product,
max_predictions=max_predictions,
timeout=timeout,
silent=True)
stop_loader(identifier)
pathways[(host, model)] = predicted_pathways
self.__display_pathways_information(
predicted_pathways, host, model)
return pathways
def _data_frame(solution):
notice("%s: %f" % self.solutions.axes[0][solution - 1][0])
notice("%s: %f" % self.solutions.axes[0][solution - 1][1])
display(self.solutions.iloc[solution - 1])