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YosefLab / Compass

In-Silico Modeling of Metabolic Heterogeneity using Single-Cell Transcriptomes
BSD 3-Clause "New" or "Revised" License
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Using a different metabolic model (e.g. Recon3D) #33

Open Hrovatin opened 3 years ago

Hrovatin commented 3 years ago

What needs to be done to use a different metabolic model (e.g. Recon3D)? is it enough if I just add a new dir with xml model into the Resources and a new model option in arg-parsing of main or is there something else I need to change?

Hrovatin commented 3 years ago

I have tried supping different xml, but now I have noticed that some reactions that do not have associated genes have a compass score. How is this possible? Is this even correct?

The same also happened when using Recon2_mat

raman91 commented 3 years ago

Hi @Hrovatin, how to use different metabolic model apart from the model incorporated in compass tool by default? Thanks

Hrovatin commented 3 years ago

I just did what I described in the first comment, but not 100% sure if that is a correct way to add a new model.

raman91 commented 3 years ago

Thanks. I ran on a different model but getting an error : multiprocessing.pool.MaybeEncodingError: Error sending result: '<multiprocessing.pool.ExceptionWithTraceback object at 0x7fac7a605e80>'. Reason: 'TypeError("cannot pickle 'SwigPyObject' object")'. Do you know how to solve this ?? Thanks

sangderk commented 2 years ago

Refer to https://github.com/YosefLab/Compass/issues/60 for the solution.