iqbal-lab / Mykrobe-predictor

Antibiotic resistance predictions in minutes on a laptop
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Request: save the .json file for later use #141

Closed RaSieb closed 5 years ago

RaSieb commented 6 years ago

With the latest commit, the .json formatted output is not separated anymore. This makes it difficult to parse the actual output (without debug messages etc.) for further use, as well as for piping.

Is there a way the actual .json file could be saved to disk, or the return could be separated into stdout and stderr?

iqbal-lab commented 6 years ago

cc @rffrancon @Phelimb

idolawoye commented 5 years ago

Hello, I have similar request as the OP so I just want to know if there is a way to go about that now as I run my analysis on the commandline and it will be great if we can have the output in a .json file saved on the hard disk.

iqbal-lab commented 5 years ago

Hi there - is there a reason, if running on the command line, you cannot save stdout? Anyway, we're about to make a big release, will take this feedback

iqbal-lab commented 5 years ago

I'll close this as you have a workaround (write stdout to a file). The new release already has a commandline option to allow you to write to a file, so you'll have that too soon