Feat: add rank lineage

[Midnighter]

• [x] fix #126
• [x] description of feature/fix
• [x] tests added/passed
• [x] add an entry to the changelog

[codecov-commenter]

Codecov Report

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

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

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Additional details and impacted files

```diff @@ 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](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/130?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None) | Coverage Δ | | |---|---|---| | [src/taxpasta/infrastructure/cli/merge.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/130?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2NsaS9tZXJnZS5weQ==) | `52.60% <0.00%> (-2.22%)` | :arrow_down: | | [src/taxpasta/infrastructure/cli/standardise.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/130?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2NsaS9zdGFuZGFyZGlzZS5weQ==) | `32.29% <0.00%> (-2.54%)` | :arrow_down: | | [src/taxpasta/domain/service/taxonomy\_service.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/130?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2RvbWFpbi9zZXJ2aWNlL3RheG9ub215X3NlcnZpY2UucHk=) | `100.00% <100.00%> (+3.70%)` | :arrow_up: | | [...tructure/domain/service/taxopy\_taxonomy\_service.py](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/130?src=pr&el=tree&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None#diff-c3JjL3RheHBhc3RhL2luZnJhc3RydWN0dXJlL2RvbWFpbi9zZXJ2aWNlL3RheG9weV90YXhvbm9teV9zZXJ2aWNlLnB5) | `73.78% <100.00%> (+73.78%)` | :arrow_up: | ... and [2 files with indirect coverage changes](https://app.codecov.io/gh/taxprofiler/taxpasta/pull/130/indirect-changes?src=pr&el=tree-more&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=None)

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[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...)