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brianjamesschmidt / gim3e

Gene Inactivation Moderated by Metabolism, Metabolomics, and Expression (COBRApy)
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Examples fail #8

Closed bollepel closed 7 years ago

bollepel commented 7 years ago

I'm totally new to GIM3E, so I tried the examples from the examples folder. I changed the solver to gurobi as I don't have a cplex license and sadle both examples give errors concerning turnover metabolites.

01_run_gim3e_with_salmonella.py results in the following output/error:

Determining the best objective value... No parameters matching 'the_problem' found ... OK Converting to irreversible... cobra/core/Reaction.py:192 UserWarning: Setting reaction reversibility is ignored ... OK Adding turnover metabolites... No parameters matching 'the_problem' found No parameters matching 'the_problem' found No parameters matching 'the_problem' found No parameters matching 'the_problem' found No parameters matching 'the_problem' found Traceback (most recent call last): File "01_run_gim3e_with_salmonella.py", line 88, in trim_model = False, solver = 'gurobi') File "/usr/local/lib/python2.7/dist-packages/gim3e-1.0.2-py2.7.egg/gim3e/core/gim3e.py", line 244, in gim3e FVA_verbose = False) File "/usr/local/lib/python2.7/dist-packages/gim3e-1.0.2-py2.7.egg/gim3e/core/gim3e.py", line 2411, in test_turnover_metabolite_constraints verbose = FVA_verbose) File "/usr/local/lib/python2.7/dist-packages/gim3e-1.0.2-py2.7.egg/gim3e/core/gim3e.py", line 1057, in irreversible_flux_variability_analysis the_index = the_reactions.index(the_reaction.id) ValueError: 'TMS_26dap__LL_c' is not in list

The second example, 02_sample_core_gim3e.py results in: cobra/io/sbml.py:83 UserWarning: print_time is deprecated 8.39 No parameters matching 'the_problem' found Determining the best objective value... No parameters matching 'the_problem' found ... OK Converting to irreversible... cobra/core/Reaction.py:192 UserWarning: Setting reaction reversibility is ignored ... OK No microarray data given, not imposing constraint based on intensity data. About to run FVA. No parameters matching 'the_problem' found No parameters matching 'the_problem' found No parameters matching 'the_problem' found Traceback (most recent call last): File "02_sample_core_gim3e.py", line 54, in trim_model = False, solver = 'gurobi') File "/usr/local/lib/python2.7/dist-packages/gim3e-1.0.2-py2.7.egg/gim3e/core/gim3e.py", line 372, in gim3e verbose = FVA_verbose) File "/usr/local/lib/python2.7/dist-packages/gim3e-1.0.2-py2.7.egg/gim3e/core/gim3e.py", line 1057, in irreversible_flux_variability_analysis the_index = the_reactions.index(the_reaction.id) ValueError: 'ACALD' is not in list

bollepel commented 7 years ago

I've found the issue. On line 1057 in gim3e.py the_reaction is already referring to a reaction id, and hence it has no attribute 'id'. Removing the .id solves the problem.