Unable to run the "test_flux_map.py" script

[PK1617]

I have repeatedly failed to run the "test_flux_map.py" both in the Python Shell and in the Anacoda/Jupiter. I run the script exactly as it is but I do not get anything. And when I am trying to call the "test_flux_map" function I get errors. Am I missing something? I have downloaded all the necessary packeges.

[pstjohn]

the test_flux_map.py file is a pytests unittest file, and isn't necessarily meant for public use. If you install pytest into your python environment, you should be able to run it without errors though.

I would instead look through and see if you can run notebooks in the 'examples' directory.

[PK1617]

Thank you for the immediate reply. I managed to run the code through the Jupyter Notebook but without the fixtures. As a follow up question I would like to ask whether we can change the thickness of the lines (apart from the dashed lines for the knocked out reactions) according to their values. I change the fluxes in the code but do not see any difference in the lines.

[pstjohn]

the simplest way is just making sure the model has a solution before calling flux_map, like in https://github.com/pstjohn/d3flux/blob/master/d3flux/examples/putida/putida_layout.ipynb.

The alternative is you can pass specific fluxes to be plotted using flux_dict, that just wants a dict-like object mapping reaction IDs to flux values.

sol = model.optimize()
d3f.flux_map(model, flux_dict=sol.fluxes)

[PK1617]

Thank you very much! The last thing I would like to ask is whether you can request the fluxes to be straight lines instead of curved. Or if you can generally manipualte the shape of the fluxes (as curved lines will be needed for cycles like the TCA cycle etc.). I assigned the coordinates of the metabolites in order to get the desired network but the fluxes come out to be very curvy.

[pstjohn]

There's a button in the lower left called 'show reaction nodes'. If you press that, you can click + drag the reaction nodes into place, and they'll stay in position if you save the json file and load it again.