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FlyBase / flybase-ontology-scripts

Scripts for working with FlyBase ontologies, currently mostly for report generation.
MIT License
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Refactored to move FCA spreadsheet gen code into separate functions #2

Closed dosumis closed 4 years ago

dosumis commented 4 years ago

To run as before - use FCA_spreadsheet_runner.py FCA_spreadsheets.py now has functions that allow running from iri_list, single_term or iri_list file.

Haven't yet added any additional tests.

Consider renaming FCA_spreadsheets.py to FCA_spreadsheet_tools.py

dosumis commented 4 years ago

@Clare72 - please review

dosumis commented 4 years ago

Some more notes on edit:

I tried to change as little code and functionality as possible. I did do quite a bit of reformatting though so change might look more than they are.

dosumis commented 4 years ago

Working on some tests and tweaks. Please don't merge yet.

Clare72 commented 4 years ago

Made some edits to comments/docstrings and renamed FCA_spreadsheets.py as suggested - no edits to code.

Clare72 commented 4 years ago

BTW, I seem to have already offered you admin access for FlyBase/flybase-ontology-scripts (says awaiting response).

dosumis commented 4 years ago

Tests now passing. Any questions about changes?

Clare72 commented 4 years ago

I can still run it to make a spreadsheet, so working fine. I was previously thinking of going the other way and grabbing fbbt from github by default, rather than a user-defined local file, but this looks good. Thanks for tidying up.

dosumis commented 4 years ago

I was previously thinking of going the other way and grabbing fbbt from github by default, rather than a user-defined local file, but this looks good. Thanks for tidying up.

Could add that as an optional keyword arg.