parklab / MuSiCal

A comprehensive toolkit for mutational signature analysis

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Refitting example

mandronescu opened this issue · comments

Hello,

I am trying to use the refitting example, however, I cannot find "musical.refit" in the package. Should I use "musical.assign" or "musical.assign_grid"?

Thank you!

Hi,

Thanks for trying out our package. The refit module can be accessed through musical.refit, and the refit function within that module can be called with musical.refit.refit(), as was used in the refitting example. Perhaps that solves the issue?

Hello, thank you for the prompt response.
It looks like the package doesn't install correctly, because __init__.py under the installation directory didn't have refit under __all__, so I was getting AttributeError: module 'musical' has no attribute 'refit'. I added refit manually, and it works.

Also, the catalog data doesn't get copied either, so musical.load_catalog() didn't find the .csv files. I copied them manually and it works.

Thank you.

Hi, the catalog issue is resolved in #71. If you uninstall, clone the most updated repo, and install again, it should work. Apologies for that.

I don't fully understand the refit issue though. Maybe I'm missing something, but in __init__.py, the module musical.refit is referred to, which means that all functions within musical.refit, including musical.refit.refit() is callable. Could you send the code that you are running which can reproduce the error? Thanks.

I reinstalled, and both the catalog and the refit module work now.

Thank you for a great tool!

Sounds good. Glad it's resolved with the reinstallation.