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fix uncertain insertion #10

Merged
merged 6 commits into from
Oct 16, 2024
Merged

fix uncertain insertion #10

merged 6 commits into from
Oct 16, 2024

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nokara26
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@nokara26 nokara26 commented Sep 25, 2024

I fixed ins unknown repeat description.
I referred following format:

@totakke
g.1134_1135ins(100) is older hgvs nomenclature?

@nokara26 nokara26 self-assigned this Sep 25, 2024
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codecov bot commented Sep 25, 2024

Codecov Report

Attention: Patch coverage is 89.18919% with 4 lines in your changes missing coverage. Please review.

Project coverage is 89.05%. Comparing base (2a7d403) to head (e11455b).
Report is 1 commits behind head on master.

Files with missing lines Patch % Lines
src/clj_hgvs/mutation.cljc 89.18% 0 Missing and 4 partials ⚠️
Additional details and impacted files
@@            Coverage Diff             @@
##           master      #10      +/-   ##
==========================================
+ Coverage   89.03%   89.05%   +0.01%     
==========================================
  Files           5        5              
  Lines        1824     1845      +21     
  Branches      127      129       +2     
==========================================
+ Hits         1624     1643      +19     
  Misses         73       73              
- Partials      127      129       +2     
Flag Coverage Δ
89.05% <89.18%> (?)

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@totakke
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totakke commented Oct 11, 2024

g.1134_1135ins(100) is older hgvs nomenclature?

Yes. You can see it in the following archive site.

see Uncertain; when the postion and/or the sequence of an inserted sequence has not been defined, a description may have a format like g.(100_150)ins(25)
https://archive.hgvs-nomenclature.org/recommendations/DNA/variant/insertion/

It got probably deprecated at some point.
I feel like we should add a new repairer (clj-hgvs.repairer) from g.1134_1135ins(100) to g.1134_1135insN[100].

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nokara26 commented Oct 15, 2024

@totakke
Thank you for reply and review!
I added unknown repeat repairer: 4307618

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Thank you so much for following the HGVS specification and preparing a repairer to migrate an old expression. 🙇
I have left a couple of comments, and also please bump the version up to 0.5.0-SNAPSHOT.

;; g.1134_1135ins(100) -> g.1134_1135insN[100]
;; r.431_432ins(5) -> r.431_432insn[5]
;; p.R78_G79ins23 -> p.R78_G79insX[23]
(defn ^:no-doc replace-unknown-repeated-seq
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The description like insN[100] does not mean repeated sequences. It expresses an uncertain inserted sequence. I feel like replace-uncertain-bases is proper naming.

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fix in this commit: b551792

@@ -624,20 +624,28 @@
;;; e.g. g.6775delinsGA
;;; g.6775delTinsGA
;;; c.145_147delinsTGG
;;; c.145_147delinsN[10]
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Though only a reference page of DNA deletion-insertion have an example of uncertain insertion, theoretically, RNA deletion-insertion and protein deletion-insertion can also have the uncertain insertion. Mutalyzer supports delinsn, e.g. https://mutalyzer.nl/normalizer/NM_004006.2:r.2623_2803delinsn. Implementation of the uncertain insertion for only DNA deletion-insertion seems incomplete 🤔

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nokara26 commented Oct 16, 2024

@totakke
Thank you for review!
I fixed rna and protein indel and support ins-format: 4a0f788
And bump the version up: 36d828d

@nokara26 nokara26 requested a review from totakke October 16, 2024 01:21
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Perfection! Thank you so much 👍

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Thank you for your review, @totakke! 🙏

I have no additional points to add. Thanks!

@federkasten federkasten merged commit 0fa3c0f into master Oct 16, 2024
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@federkasten federkasten deleted the fix/fix-ins-unkown-repeat branch October 16, 2024 02:52
@nokara26 nokara26 changed the title fix ins unkown repeat fix uncertain ins and delins Oct 16, 2024
@nokara26 nokara26 changed the title fix uncertain ins and delins fix uncertain insertion Oct 16, 2024
@nokara26 nokara26 mentioned this pull request Oct 16, 2024
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3 participants