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fix: fix protein-insertion regex #13

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merged 1 commit into from
Dec 5, 2024
Merged

fix: fix protein-insertion regex #13

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3 changes: 2 additions & 1 deletion src/clj_hgvs/mutation.cljc
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Original file line number Diff line number Diff line change
Expand Up @@ -1760,6 +1760,7 @@
;;;
;;; e.g. Lys23_Leu24insArgSerGln
;;; Arg78_Gly79insX[23]
;;; Thr89_Ter90insSerProIle (T89_*90insSPI)

(defrecord ProteinInsertion [ref-start coord-start ref-end coord-end alts]
Mutation
Expand Down Expand Up @@ -1819,7 +1820,7 @@
vec)))

(def ^:private protein-insertion-re
#"([A-Z](?:[a-z]{2})?)(\d+)_([A-Z](?:[a-z]{2})?)(\d+)ins([\da-zA-Z*\[\]]+)")
#"([A-Z](?:[a-z]{2})?)(\d+)_([A-Z*](?:[a-z]{2})?)(\d+)ins([\da-zA-Z*\[\]]+)")

(defn parse-protein-insertion
[s]
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13 changes: 11 additions & 2 deletions test/clj_hgvs/mutation_test.cljc
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Original file line number Diff line number Diff line change
Expand Up @@ -1371,6 +1371,11 @@
(def protein-insertion4 (mut/protein-insertion "Arg" (coord/protein-coordinate 78)
"Gly" (coord/protein-coordinate 79)
["Xaa" "Xaa" "Xaa" "Xaa" "Xaa" "Xaa" "Xaa" "Xaa" "Xaa" "Xaa"]))
(def protein-insertion5s "Thr89_Ter90insSerProIle")
(def protein-insertion5ss "T89_*90insSPI")
(def protein-insertion5 (mut/protein-insertion "Thr" (coord/protein-coordinate 89)
"Ter" (coord/protein-coordinate 90)
["Ser" "Pro" "Ile"]))

(deftest format-protein-insertion-test
(testing "returns a string expression of a protein insertion"
Expand All @@ -1386,7 +1391,9 @@
protein-insertion3 {:ins-format :count} protein-insertion3sc
protein-insertion3 {:amino-acid-format :short :ins-format :count} protein-insertion3scs
protein-insertion4 {:ins-format :auto} protein-insertion4sc
protein-insertion4 {:amino-acid-format :short :ins-format :auto} protein-insertion4scs)))
protein-insertion4 {:amino-acid-format :short :ins-format :auto} protein-insertion4scs
protein-insertion5 nil protein-insertion5s
protein-insertion5 {:amino-acid-format :short} protein-insertion5ss)))

(deftest parse-protein-insertion-test
(testing "returns a correct ProteinInsertion"
Expand All @@ -1400,7 +1407,9 @@
protein-insertion3sc protein-insertion3
protein-insertion3scs protein-insertion3
protein-insertion4sc protein-insertion4
protein-insertion4scs protein-insertion4))
protein-insertion4scs protein-insertion4
protein-insertion5s protein-insertion5
protein-insertion5ss protein-insertion5))
(testing "invalid protein insertion"
(are [s] (thrown? #?(:clj Throwable, :cljs js/Error)
(mut/parse-protein-insertion s))
Expand Down