qiime2 / q2-feature-table

QIIME 2 plugin supporting operations on feature tables.
BSD 3-Clause "New" or "Revised" License
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BUG: improve error message formatting in `feature-table tabulate-seqs` #298

Closed lizgehret closed 9 months ago

lizgehret commented 9 months ago

Bug Description When running feature-table tabulate-seqs, it's possible to generate the following error using the PD Mice data when using the default merge method of strict: Screen Shot 2023-12-19 at 10 51 36 AM

The error message is correct, but the formatting looks clunky due to an unnecessary newline.

Steps to reproduce the behavior

  1. Download the following artifacts from the PD Mice tutorial:

  2. Keeping all of the above artifacts in the same working directory, put the two taxonomy artifacts into a sub directory of your choice (e.g. multi-taxonomy/ or something like that)

  3. Run the following command (using a QIIME 2 Amplicon 2023.9 environment):

    qiime feature-table tabulate-seqs \
    --i-data dada2_rep_set.qza \
    --i-taxonomy multi-taxonomy/ \
    --o-visualization dada2_multi_taxonomy.qzv \
    --verbose

    The error in the above screenshot will be displayed (since the --p-merge-method has a default of strict).

Expected behavior This isn't strictly a bug, but the formatting of the error message looks a bit weird, and can be fixed with an updated multi-line string.

I'll leave the rest to you to figure out @hagenjp 😉