cooperlab / tcgaintegrator Goto Github PK

I keep getting this error.
I installed fbget independently too, but doesnt seem to work.

Traceback (most recent call last): File "BuildDataset.py", line 1, in <module> from firebrowse import fbget ImportError: cannot import name fbget

I see a .mat file as output.
How do I use this in Python. Seems like this Matlab compatible file and not pickle file.

Is it possible to extract features of DNA methylation from the selected TCGA tumor samples?

After entering into the "Integrator" virtualenv and installing dependencies (requests and firebrowse), when trying to use TCGAIntegrator it returns the following error:

Traceback (most recent call last): File "<stdin>", line 1, in <module> File "tcgaintegrator/__init__.py", line 4, in <module> from .BuildDataset import BuildDataset File "tcgaintegrator/BuildDataset.py", line 1, in <module> from firebrowse import fbget

I can import firebrowse itself, but cannot import fbget in any way (I tried from firebrowse import fbget and import fbget). I don't know if the latest version of firebrowse module has changed from the older ones.

In the broad website they say you should use https://confluence.broadinstitute.org/display/GDAC/fbget#fbget-configuration but with 0.1.11 I'm unable to do this also.