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feat: added a repairer for protein insertion to extension #4

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May 30, 2021
Merged

feat: added a repairer for protein insertion to extension #4

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12 changes: 11 additions & 1 deletion src/clj_hgvs/repairer.cljc
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Original file line number Diff line number Diff line change
Expand Up @@ -276,6 +276,15 @@
(string/replace s #"extTer(\?|\d+)$" "ext*$1")
s))

;; p.S733_*734insS -> p.*734Sext*?
(defn ^:no-doc ins->ext
[s kind]
(if (= kind :protein)
(string/replace s
#"[A-Z](\d+_\*)(\d+)ins([A-Z]+[a-z]*)"
"*$2$3ext*?")
s))

(def built-in-repairers
"The built-in repair functions.

Expand Down Expand Up @@ -323,4 +332,5 @@
remove-fs-greater
protein-ter-substitution->ext
frameshift->ext
ext-ter->downstream])
ext-ter->downstream
ins->ext])
5 changes: 4 additions & 1 deletion test/clj_hgvs/core_test.cljc
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Expand Up @@ -364,7 +364,10 @@
"p.*833fs" "p.*833ext*?"

;; ext-ter->downstream
"p.Ter397ThrextTer?" "p.Ter397Thrext*?")
"p.Ter397ThrextTer?" "p.Ter397Thrext*?"

;; ext->ins
"p.S733_*734insS" "p.*734Sext*?")

(are [s] (let [s* (hgvs/repair-hgvs-str s)]
(and (= s* s) (some? (hgvs/parse s*))))
Expand Down