Repair illegal substitutions to an inversion

[nuggetoriniku]

I added two repairer functions to correct illegal hgvs strings.
Could you review this?

[codecov]

Codecov Report

Merging #3 into master will increase coverage by 0.08%.
The diff coverage is 100.00%.

@@            Coverage Diff             @@
##           master       #3      +/-   ##
==========================================
+ Coverage   88.96%   89.04%   +0.08%     
==========================================
  Files           5        5              
  Lines        1803     1817      +14     
  Branches      127      127              
==========================================
+ Hits         1604     1618      +14     
  Misses         72       72              
  Partials      127      127              

Impacted Files	Coverage Δ
src/clj_hgvs/repairer.cljc	100.00% <100.00%> (ø)

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[totakke]

Thank you for PR. I added some comments. And you should add test cases to clj-hgvs.core-test/repair-hgvs-str-test.

[totakke]

I cannot understand the necessity of this repair rule. The repair case written as the comment is covered by existing substitutions->delins.

(require '[clj-hgvs.core :as hgvs]
         '[clj-hgvs.repairer :as repairer])

(hgvs/repair-hgvs-str "c.233_234TC>CT" [repairer/substitutions->delins])
;;=> "c.233_234delTCinsCT"

If you want to omit the deletion bases, you can use :show-bases? false option.

(-> (hgvs/parse "c.233_234delTCinsCT")          
    (hgvs/format {:show-bases? false}))
;;=> "c.233_234delinsCT"

[nuggetoriniku]

Thank you for your review.
I removed substitutions->delins* function.

[totakke]

An inversion mutation is not appeared in protein mutations.

(if (#{:genome :mitochondria :coding-dna :non-coding-dna :circular-dna :rna}
     kind)
  ...
  s)

[nuggetoriniku]

I set the condition for exclude :protein

[totakke]

Rename to substitutions->inv and add it to above substitution->delins in built-in-repairers.

[nuggetoriniku]

I renamed to substitutions->inv and added it in built-in-repairers.

[totakke]

The regex does not cover all coordinate patterns. Additionally, I recommend using replace fn.

(letfn [(revcomp [s]
          (->> (reverse s)
               (map {\A \T \T \A \C \G \G \C})
               (apply str)))]
  (string/replace s
                  #"([-\d+*]+_[-\d+*]+)([A-Z]{2,})>([A-Z]{2,})"
                  (fn [[s coords del ins]]
                    (if (= del (revcomp ins))
                      (str coords "inv")
                      s))))

[nuggetoriniku]

I fixed the regex to cover all coordinate patterns, and changed process with using replace fn.

[totakke]

Thanks, your fix is perfect, but a test is still missing (#3 (review)).

Could you add c.2210_2211CA>TG -> c.2210_2211inv test case to just above the following line?

clj-hgvs/test/clj_hgvs/core_test.cljc

Line 286 in a920313

;; substitution->delins

[totakke]

LGTM. I plan to merge it after @federkasten approval.

[federkasten]

Sorry for the delay in reviewing.
I have checked. No additional comments. Thanks! 👍