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raphael-group / decifer

DeCiFer is an algorithm that simultaneously selects mutation multiplicities and clusters SNVs by their corresponding descendant cell fractions (DCF).
BSD 3-Clause "New" or "Revised" License
20 stars 7 forks source link

create input issue #3

Closed mkinnaman closed 3 years ago

mkinnaman commented 3 years ago

Hi,

I am having trouble with the create_input.ipynb - I am getting a json formatting error when trying to open in jupyter.

I ran the code through a validator and got the following errors: `The JSON input is NOT valid according to RFC 4627 (JSON specification). Unexpected token \t")\n" at position 3706.

Close The JSON input is NOT valid in JavaScript, illegal character: \ (At line #98), (At position #45)`

THanks, Michael

simozacca commented 3 years ago

Thank you for this catch! @brian-arnold could please check what is going wrong? It might be related to the new version?

Also, @brian-arnold it seems that the script does not load in the github page, could you please try to re-create and push it after you have run it completely?

brian-arnold commented 3 years ago

Hi @mkinnaman, apologies for the bug. The notebook has been updated and worked on my end, but please let us know if you're still encountering problems. Thanks!

mkinnaman commented 3 years ago

@brian-arnold no worries!

Would you be able to put example input files for the script in this repository? I am importing data from other callers and I am having trouble running the script on my data as it doesn't look like I have it formatted correctly.

Thanks!