# -*- coding: utf-8 -*-
"""Contains function to identify the type of boundary reactions.
This module uses various heuristics to decide whether a boundary reaction
is an exchange, demand or sink reaction. It mostly orientates on the following
paper:
Thiele, I., & Palsson, B. Ø. (2010, January). A protocol for
generating a high-quality genome-scale metabolic reconstruction.
Nature protocols. Nature Publishing Group.
http://doi.org/10.1038/nprot.2009.203
"""
import logging
from collections import Counter
import pandas as pd
from cobra.medium.annotations import compartment_shortlist, excludes, sbo_terms
[docs]LOGGER = logging.getLogger(__name__)
[docs]def find_external_compartment(model):
"""Find the external compartment in the model.
Uses a simple heuristic where the external compartment should be the one
with the most exchange reactions.
Arguments
---------
model : cobra.Model
A cobra model.
Returns
-------
str
The putative external compartment.
"""
if model.boundary:
counts = pd.Series(tuple(r.compartments)[0] for r in model.boundary)
most = counts.value_counts()
most = most.index[most == most.max()].to_series()
else:
most = None
like_external = compartment_shortlist["e"] + ["e"]
matches = pd.Series(
[co in like_external for co in model.compartments], index=model.compartments
)
if matches.sum() == 1:
compartment = matches.index[matches][0]
LOGGER.info(
"Compartment `%s` sounds like an external compartment. "
"Using this one without counting boundary reactions" % compartment
)
return compartment
elif most is not None and matches.sum() > 1 and matches[most].sum() == 1:
compartment = most[matches[most]][0]
LOGGER.warning(
"There are several compartments that look like an "
"external compartment but `%s` has the most boundary "
"reactions, so using that as the external "
"compartment." % compartment
)
return compartment
elif matches.sum() > 1:
raise RuntimeError(
"There are several compartments (%s) that look "
"like external compartments but we can't tell "
"which one to use. Consider renaming your "
"compartments please."
)
if most is not None:
return most[0]
LOGGER.warning(
"Could not identify an external compartment by name and"
" choosing one with the most boundary reactions. That "
"might be complete nonsense or change suddenly. "
"Consider renaming your compartments using "
"`Model.compartments` to fix this."
)
# No info in the model, so give up
raise RuntimeError(
"The heuristic for discovering an external compartment "
"relies on names and boundary reactions. Yet, there "
"are neither compartments with recognized names nor "
"boundary reactions in the model."
)
[docs]def is_boundary_type(reaction, boundary_type, external_compartment):
"""Check whether a reaction is an exchange reaction.
Arguments
---------
reaction : cobra.Reaction
The reaction to check.
boundary_type : str
What boundary type to check for. Must be one of
"exchange", "demand", or "sink".
external_compartment : str
The id for the external compartment.
Returns
-------
boolean
Whether the reaction looks like the requested type. Might be based
on a heuristic.
"""
# Check if the reaction has an annotation. Annotations dominate everything.
sbo_term = reaction.annotation.get("sbo", "")
if isinstance(sbo_term, list):
sbo_term = sbo_term[0]
sbo_term = sbo_term.upper()
if sbo_term == sbo_terms[boundary_type]:
return True
if sbo_term in [sbo_terms[k] for k in sbo_terms if k != boundary_type]:
return False
# Check if the reaction is in the correct compartment (exterior or inside)
correct_compartment = external_compartment in reaction.compartments
if boundary_type != "exchange":
correct_compartment = not correct_compartment
# Check if the reaction has the correct reversibility
rev_type = True
if boundary_type == "demand":
rev_type = not reaction.reversibility
elif boundary_type == "sink":
rev_type = reaction.reversibility
return (
reaction.boundary
and not any(ex in reaction.id for ex in excludes[boundary_type])
and correct_compartment
and rev_type
)
[docs]def find_boundary_types(model, boundary_type, external_compartment=None):
"""Find specific boundary reactions.
Arguments
---------
model : cobra.Model
A cobra model.
boundary_type : str
What boundary type to check for. Must be one of
"exchange", "demand", or "sink".
external_compartment : str or None
The id for the external compartment. If None it will be detected
automatically.
Returns
-------
list of cobra.reaction
A list of likely boundary reactions of a user defined type.
"""
if not model.boundary:
LOGGER.warning(
"There are no boundary reactions in this model. "
"Therefore specific types of boundary reactions such "
"as 'exchanges', 'demands' or 'sinks' cannot be "
"identified."
)
return []
if external_compartment is None:
external_compartment = find_external_compartment(model)
return model.reactions.query(
lambda r: is_boundary_type(r, boundary_type, external_compartment)
)