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althonos / pyhmmer

Cython bindings and Python interface to HMMER3.
https://pyhmmer.readthedocs.io
MIT License
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Expose ppline in Alignment class #59

Closed arajkovic closed 9 months ago

arajkovic commented 9 months ago

Hi!

This PR exposes the ppline string from P7_ALIDISPLAY. We're using pyhmmer here at EBI for the new version of the HMMER web tool. While working on the alignment display, I realised that the posterior probability annotation (ppline) is missing, so adding it to the Alignment class.

Cheers!

althonos commented 9 months ago

Would you mind naming it posterior_probabilities instead of ppline, to be a bit more informative on the Python side? Thanks for the PR :smile:

codecov[bot] commented 9 months ago

Codecov Report

All modified and coverable lines are covered by tests :white_check_mark:

Comparison is base (149785c) 79.59% compared to head (ec8d6d8) 79.60%. Report is 1 commits behind head on master.

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Additional details and impacted files ```diff @@ Coverage Diff @@ ## master #59 +/- ## ======================================= Coverage 79.59% 79.60% ======================================= Files 7 7 Lines 7008 7010 +2 ======================================= + Hits 5578 5580 +2 Misses 1430 1430 ``` | [Flag](https://app.codecov.io/gh/althonos/pyhmmer/pull/59/flags?src=pr&el=flags&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Martin+Larralde) | Coverage Δ | | |---|---|---| | [v3.10](https://app.codecov.io/gh/althonos/pyhmmer/pull/59/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Martin+Larralde) | `79.60% <100.00%> (+<0.01%)` | :arrow_up: | | [v3.11](https://app.codecov.io/gh/althonos/pyhmmer/pull/59/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Martin+Larralde) | `79.60% <100.00%> (+<0.01%)` | :arrow_up: | | [v3.12](https://app.codecov.io/gh/althonos/pyhmmer/pull/59/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Martin+Larralde) | `79.60% <100.00%> (+<0.01%)` | :arrow_up: | | [v3.7](https://app.codecov.io/gh/althonos/pyhmmer/pull/59/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Martin+Larralde) | `79.57% <100.00%> (+<0.01%)` | :arrow_up: | | [v3.8](https://app.codecov.io/gh/althonos/pyhmmer/pull/59/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Martin+Larralde) | `79.60% <100.00%> (+<0.01%)` | :arrow_up: | | [v3.9](https://app.codecov.io/gh/althonos/pyhmmer/pull/59/flags?src=pr&el=flag&utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Martin+Larralde) | `79.60% <100.00%> (+<0.01%)` | :arrow_up: | Flags with carried forward coverage won't be shown. [Click here](https://docs.codecov.io/docs/carryforward-flags?utm_medium=referral&utm_source=github&utm_content=comment&utm_campaign=pr+comments&utm_term=Martin+Larralde#carryforward-flags-in-the-pull-request-comment) to find out more.

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althonos commented 9 months ago

Thanks! I'll make a new release shortly.