Feat: add rank lineage

[Midnighter]

• fix [Feature] Add --add-rank-lineage to taxpasta merge and taxpasta standardise #126
• description of feature/fix
• tests added/passed
• add an entry to the changelog

[codecov-commenter]

Codecov Report

Patch coverage: 58.82% and project coverage change: +3.08% 🎉

Comparison is base (d130751) 82.85% compared to head (79167a3) 85.93%.

❗ Current head 79167a3 differs from pull request most recent head b217f33. Consider uploading reports for the commit b217f33 to get more accurate results

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Additional details and impacted files

@@            Coverage Diff             @@
##              dev     #130      +/-   ##
==========================================
+ Coverage   82.85%   85.93%   +3.08%     
==========================================
  Files         114      114              
  Lines        1744     1778      +34     
  Branches      308      316       +8     
==========================================
+ Hits         1445     1528      +83     
+ Misses        255      202      -53     
- Partials       44       48       +4     

Files Changed	Coverage Δ
src/taxpasta/infrastructure/cli/merge.py	52.60% <0.00%> (-2.22%)	⬇️
src/taxpasta/infrastructure/cli/standardise.py	32.29% <0.00%> (-2.54%)	⬇️
src/taxpasta/domain/service/taxonomy_service.py	100.00% <100.00%> (+3.70%)	⬆️
...tructure/domain/service/taxopy_taxonomy_service.py	73.78% <100.00%> (+73.78%)	⬆️

... and 2 files with indirect coverage changes

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[jfy133]

Missing any docs updates?

Overall looks ok to me, just a few queries (but not blockers IMO)

No tested, will try now but can't guaruntee I'll get to it, I trust you ;)

[jfy133]

Which order is this meant to be in the actual file/ I typically would view the rank to go broad to specific left to right,

e.g. "Saccharomycetes;Ascomycota;Eukaryota;root", would be root;Eukaryota;Ascomycota;Saccaromycetes,

Which also makes me wonder: what happens when there are species that are 'missing' an intermediate taxonmic rank (e.g. has a species, genus, family name, but no order name...., but then continues with classes, phyla etc.)

[Midnighter]

That's a fair point. I simply used the order returned by taxopy (which makes sense from the perspective of a particular taxon). However, you're right that most tools provide the lineage from higher to more specific rank.

[jfy133]

Tested and no bugs: still works for me!

I still personally find the reversed the lineages reflexively unintuitive, but not wrong. You're welcome to merge from my POV! (once docs updated, if necessary!)

[Midnighter]

We can turn around the order of the lineages. It makes sense to me and hopefully, not too many people have built code based on this yet.

I don't actually know how taxopy reports skipped ranks in the lineage. Would need to add test data for that. Do you happen to know an example from the NCBI taxonomy?

[Midnighter]

As discussed, will merge this and make the proposed changes in a new PR.

[jfy133]

We can turn around the order of the lineages. It makes sense to me and hopefully, not too many people have built code based on this yet.

👍

I don't actually know how taxopy reports skipped ranks in the lineage. Would need to add test data for that. Do you happen to know an example from the NCBI taxonomy?

Not off the top of my head... I remember seeing it in metaphlan2 or malt results...

Maybe candidatus phyla etc?

[jfy133]

Possibly something like this: https://www.ncbi.nlm.nih.gov/Taxonomy/Browser/wwwtax.cgi?mode=Info&id=1387480&lvl=3&lin=f&keep=1&srchmode=1&unlock

(Can't check properly from my phone though...)