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Home Page: http://biosustain.github.io/driven/
License: Apache License 2.0
Data-Driven Constraint-based analysis
Home Page: http://biosustain.github.io/driven/
License: Apache License 2.0
I'm getting an error when trying to compute a condition-specific model by driven.imat
.
It seems to be an issue with optlang:
AssertionError Traceback (most recent call last)
/usr/lib/python3/dist-packages/optlang/expression_parsing.py in _parse_quadratic_expression(expression, expanded)
128 term = 1.0 * term
--> 129 assert term.is_Mul, "What is this? {}".format(type(term))
130 factors = term.args
AssertionError: What is this? <class 'optlang.gurobi_interface.Variable'>
A small example with random expression data to reproduce the problem:
import cobra.test
from numpy.random import random
from numpy import array
from numpy import percentile
import driven
model = cobra.test.create_test_model("textbook")
identifiers = [g.id for g in model.genes]
conditions = ["test"]
expression = array([random(len(identifiers)) * 100]).transpose()
expression.shape == (len(identifiers), len(conditions))
exprof = driven.ExpressionProfile(identifiers, conditions, expression)
low_cutoff = percentile(expression, 25)
high_cutoff = percentile(expression, 75)
model.solver = "gurobi" # cplex
model_cond = driven.imat(model, exprof, (low_cutoff, high_cutoff), condition="test")
Although this error occurs with gurobi and cplex set as solver, it works fine with glpk (in reasonable time only for smaller models).
I tried python 2 and 3. The optlang package is the latest version (1.4.4)
I tried to install driven but I see the current version of its dependencies and the changes that came along with them broke the installation.
The error I am getting is related to cameo dependency:
Traceback (most recent call last):
File "d:\Coding\Repositories\Rejuvenatebiomed\Jupyter\cobrapy\iMAT.py", line 1, in <module>
from driven.flux_analysis.transcriptomics import gimme, imat
File "C:\Python39\lib\site-packages\driven\flux_analysis\transcriptomics.py", line 22, in <module>
from cameo.core.solver_based_model import SolverBasedModel
ModuleNotFoundError: No module named 'cameo.core.solver_based_model'
This is because, in the current release of cameo, there's no such thing as cameo.core.solver_based,
Since this could represent an issue with other dependencies as well, could you provide all the right / tested version of the dependencies with which you tested driven (a list with the versions or, ideally, a docker image)
Thank you,
Roland
I am trying to integrate both transcriptomic and metabolomic data into an E.coli model (Escherichia coli str. K-12 substr. MG1655, model iML1515). However, when using gim3e function, the solver becomes infeasible after the first slim_optimize, the one to obtain the penalty_bound_constraint.
I have changed the solver to cplex and the error that i get is:
cplex.exceptions.errors.CplexSolverError: CPLEX Error 1225: Numeric entry is not a double precision number (NaN).
This error comes from this line (144 if not mistaken):
model.objective = objective
However the origin of the error comes from:
# Penalty bound constraint
penalty_obj = model.slim_optimize()
When trying to optimize the model after resetting the objective function, the solver status changes to infeasible, making variable penalty_obj equal to nan and so the constraint that is built after gets this value as an upper_bound.
My inputs are the ones requested:
I have already tried a less complex model, expression profile and fewer metabolites.
I uploaded a zip with 3 files:
Notes: Cplex solver was used but if the attempt to reproduce is done with glpk the infeasible error still happens. The python version was 3.8.5.
I encountered an error when calling the imat function:
imat(recon, exprof, (0, 30), condition="cond1")
[...]
TypeError: Call constructor takes at most 3 positional arguments
I can track it down to a sympy call by parse_expr
:
./driven/data_sets/expression_profile.py in _map_gene_to_rxn(self, reaction, gene_values, by)
333 rule = reaction.gene_reaction_rule.replace("and", "*").replace("or",
334 "+")
--> 335 expression = parse_expr(rule, local_dict)
336 if by == "or2max_and2min":
337 expression = expression.replace(Mul, Min).replace(Add, Max)
A minimal example to reproduce the error would be:
from sympy import Symbol
from sympy.parsing.ast_parser import parse_expr
local_dict = {'5161.0': 5161.0,
'1738.0': 1738.0,
'5160.0': 5160.0,
'1737.0': 1737.0,
'5162.0': 5162.0,
'8050.0': 8050.0}
rule = '(1738.0 * 8050.0) * (5161.0 * 5162.0) * (1737.0) + (1738.0 * 8050.0) * (5160.0 * 5162.0) * (1737.0)'
expression = parse_expr(rule, local_dict)
[...]
TypeError: Call constructor takes at most 3 positional arguments
Do you have any clue what's going on here?
extended log file
python 3.7.2+
sympy 1.3
from driven import ExpressionProfile
Traceback (most recent call last):
File "", line 1, in
ImportError: cannot import name ExpressionProfile
Got the same thing in both python 2.7 and 3.5.3
is there any alternative to load expression data without ExpressionProfile
?
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