Closed weinstockj closed 4 years ago
Hi,
The run_maf
function does a little bit of pre-processing specific to the Mutation Annotation File (maf) format that parses the inputs, generates spectra, etc. As of now, we have the input for this from the python api as a string for a path leading to a file.
However, if you want to run just the algorithm itself, you can call bnmf
found here https://github.com/broadinstitute/getzlab-SignatureAnalyzer/blob/7e18db8bf84aae8e0273b1052df84ec969c8c5de/signatureanalyzer/bnmf.py#L20
This will take a DataFrame. We could add an enhancement for the python API to take in either a file-path or a DataFrame in the future.
Best,
Shankara
Great, thanks so much for your consideration. My suggestion was more alluding to documentation (rather than a feature request).
Thanks, we can clarify this in the README. It does not specify what input.maf
is as of now.
Hi SignatureAnalyzer developers,
I attempted to run
sa.run_maf
with a Pandas dataframe as the first argument instead of a string. Doing so resulted in. Inspecting source indicates that the object is directly passed into pd.read_csv (https://github.com/broadinstitute/getzlab-SignatureAnalyzer/blob/master/signatureanalyzer/signatureanalyzer.py#L85)
I tried this approach (DataFrame argument instead of file path) as it was suggested by the README code:
Thanks for developing SignatureAnalyzer, Josh