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brianjamesschmidt / gim3e

Gene Inactivation Moderated by Metabolism, Metabolomics, and Expression (COBRApy)
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import statement outdated? #3

Closed sshameer closed 8 years ago

sshameer commented 8 years ago

Hi

I found "..flux_analysis.objective import update_objective" in gim3e_optimize function from gim3e.core.gim3e.py

I think the latest version of cobrapy does not have "objective" in "flux_analysis"

Thank you for this package Keep up the good work Sanu

result = gim3e.gim3e(cobra_model,expData) Switched solver from cplex to glpk. Determining the best objective value... Traceback (most recent call last): File "", line 1, in File "/usr/local/lib/python2.7/dist-packages/gim3e-1.0.3-py2.7.egg/gim3e/core/gim3e.py", line 148, in gim3e tolerance_integer = tolerance_integer) File "/usr/local/lib/python2.7/dist-packages/gim3e-1.0.3-py2.7.egg/gim3e/core/gim3e.py", line 2047, in gim3e_optimize from cobra.flux_analysis.objective import update_objective

ImportError: No module named objective

sshameer commented 8 years ago

Hi aebrahim

Thanks for the quick response :+1: I think you missed deleting the import statement at line 2047

unless the import statement is not deleted, the error seems to remain

result = gim3e.gim3e(cobra_model,expData) Switched solver from cplex to glpk. Determining the best objective value... Traceback (most recent call last): File "", line 1, in File "/usr/local/lib/python2.7/dist-packages/gim3e-1.0.3-py2.7.egg/gim3e/core/gim3e.py", line 148, in gim3e tolerance_integer = tolerance_integer) File "/usr/local/lib/python2.7/dist-packages/gim3e-1.0.3-py2.7.egg/gim3e/core/gim3e.py", line 2047, in gim3e_optimize from cobra.flux_analysis.objective import update_objective ImportError: No module named objective

Deleting the import fixes this issue