ENH: Add busco-results input to dereplicate-mags

[VinzentRisch]

solves #161

• Adds metadata and metadata_column parameters to dereplicate-mags.
• If metadata and metadata_column parameters are provided the bin with the highest value in that column is chosen. If there is a tie then the longest bin is chosen.

[codecov]

Codecov Report

All modified and coverable lines are covered by tests ✅

Project coverage is 95.64%. Comparing base (b6d068a) to head (a18c138).
Report is 5 commits behind head on main.

Additional details and impacted files

@@            Coverage Diff             @@
##             main     #213      +/-   ##
==========================================
+ Coverage   95.60%   95.64%   +0.04%     
==========================================
  Files          34       34              
  Lines        1956     1975      +19     
  Branches      226      229       +3     
==========================================
+ Hits         1870     1889      +19     
  Misses         48       48              
  Partials       38       38              

☔ View full report in Codecov by Sentry.
📢 Have feedback on the report? Share it here.

[misialq]

Hey @VinzentRisch, nice work, thanks! See some suggestions below :)

[misialq]

Hey @VinzentRisch, seems like there was a coverage failure and this time I think it's correct - could you please investigate and address accordingly? 🙏

[VinzentRisch]

Hi Michal
Now the coverage should be sorted out.
I have a question. Now the user can choose any metadata column and how its set up now the highest value in that column is used for dereplication.
Can you see any case where a user would want the lowest value in a column for dereplication.
I could add another parameter that would specify if the user wants the highest or the lowest value in the column. Do you see an application for that?

[misialq]

Hey @VinzentRisch, excellent question - thanks for bringing that up! I think there may be some cases like this, although not with BUSCO. For example, CheckM has a contamination score: if a user was to present a table with those results, they may want to pick MAGs with the lowest value of contamination. So your suggestion makes sense - it would be nice if you introduce one more param and maybe set it to 'max' by default. 🚀

Copilot reviewed 3 out of 4 changed files in this pull request and generated 1 suggestion.

Files not reviewed (1)

• q2_moshpit/dereplication/tests/data/busco_results.tsv: Language not supported

Comments skipped due to low confidence (3)

q2_moshpit/dereplication/tests/test_dereplication.py:150

• Add a test case to ensure that the dereplicate_mags function works correctly when metadata and metadata_column are provided.

obs_mags, obs_pa = dereplicate_mags(mags, self.dist_matrix, threshold=0.99)

q2_moshpit/dereplication/derep.py:300

• The walrus operator ':=' is used, which is not available in Python versions prior to 3.8. Ensure compatibility with the required Python version or avoid using the walrus operator.

values := metadata_column[bins]

q2_moshpit/dereplication/derep.py:293

• [nitpick] The error message could be more specific. Consider changing it to 'The specified metadata column must contain numerical values.'

raise ValueError('The specified metadata column has to be numerical.')

[misialq]

Looks good, thanks @VinzentRisch!