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Command line implementation of get_expression_data() #70

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rmarkello opened this issue Aug 14, 2019 · 0 comments · Fixed by #82
Closed

Command line implementation of get_expression_data() #70

rmarkello opened this issue Aug 14, 2019 · 0 comments · Fixed by #82
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enhancement New feature or request

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@rmarkello
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The issue

The abagen.get_expression_data() function is the primary workflow of use in the abagen toolbox. Right now, everything else in the toolbox (besides the abagen.mouse module) supports that function. It might be nice, therefore, to allow access to the function via the command line instead of having to use it from within a Python terminal session for those who are less comfortable with Python.

Proposed solution

Add a CLI for abagen.get_expression_data() that allows users to point to their atlas image file and specify an output CSV file for the dataframe(s) returned by the function. I'm imaging something like:

abagen --output expression.csv my_atlas.nii.gz

which would use my_atlas.nii.gz to generate a region x gene dataframe that is saved to expression.csv in the current directory.

All the parameters of the function should be accessible via optional arguments to the function, and I am happy to discuss / iterate on the actual command name itself, but this might be a nice feature for some users!

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