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biocore / metagenomics_pooling_notebook

Jupyter notebooks to assist with sample processing
MIT License
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WIP: Fixed empty tm300_8_tool/tm50_8_tool columns. #99

Closed charles-cowart closed 1 year ago

charles-cowart commented 1 year ago

generate_qiita_prep_file() renames certain columns, adds empty columns for missing columns, and reorders them before returning the df to the user. In this case, if tm300_8_tool and tm50_8_tool were instead named 'TM300 8 Tool' and 'TM50 8 Tool', they wouldn't be renamed to their proper names, two new columns with the proper names would be added, and the two old columns would be implicitly dropped in the reordering. This has been fixed.

Not yet fixed: additional columns will still be dropped. unit-tests not created.

charles-cowart commented 1 year ago

Needs unit test for the new behavior. I think it might be good to also lower-case the header of the output and raise an error if there is a duplicate, since we do that when taking the pre-prep file as input. Better to let the creator know and resolve it.

charles-cowart commented 1 year ago

Ready for review! Ty @antgonza and @mmbryant23 for their help, suggestions, and mods!