output documentation & parser

iqbal-lab / Mykrobe-predictor

Antibiotic resistance predictions in minutes on a laptop

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output documentation & parser #86

Closed stephenturner closed 8 years ago

stephenturner commented 8 years ago

Need better docs on output and JSON parser.

What do the lines in the output refer to:
- R_per_cov
- S_per_cov
- R_median_cov
- S_median_cov
- conf
Why is induced_resistant given under inferred variants, but the resistance profile shows inconclusive?

iqbal-lab commented 8 years ago

induced resistance means - this is the drug this allele causes resistance in

iqbal-lab commented 8 years ago

we could change it to "associated_drug" I suppose

Phelimb commented 8 years ago

Agree we should have some more detailed documentation somewhere though. Thoughts on where @iqbal-lab?

Maybe https://mykrobe-predictor.readme.io/docs ?

I've heard good things about readme.io.

Phelimb commented 8 years ago

Possibly overkill though.

stephenturner commented 8 years ago

a few sections in your README.md would be good enough

Stephen

On Wed, Sep 23, 2015 at 12:44 PM, Phelim Bradley notifications@github.com wrote:

Possibly overkill though.

— Reply to this email directly or view it on GitHub https://github.com/iqbal-lab/Mykrobe-predictor/issues/86#issuecomment-142658549 .

stephenturner commented 8 years ago

Thanks! :+1:

stephenturner commented 8 years ago

coming back to this, do you have any suggestions for parsing the JSON files? what about for JSON files for multiple runs? any parser to aggregate into some tabular format?

iqbal-lab commented 8 years ago

@Phelimb has some stuff - is it public yet Phelim?