fix: add unknown repeat repairer

chrovis · Oct 15, 2024 · 4307618 · 4307618
1 parent e11455b
commit 4307618
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diff --git a/src/clj_hgvs/repairer.cljc b/src/clj_hgvs/repairer.cljc
@@ -156,6 +156,20 @@
     (string/replace s #"del\d+ins" "delins")
     s))
 
+;; 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
+  [s kind]
+  (case kind
+    (:genome :mitochondria :coding-dna :non-coding-dna :circular-dna)
+    (string/replace s #"ins\((\d+)\)$" "insN[$1]")
+    (:rna)
+    (string/replace s #"ins\((\d+)\)$" "insn[$1]")
+    (:protein)
+    (string/replace s #"ins(\d+)$" "insX[$1]")
+    s))
+
 ;; c.112GAT(14) -> c.112GAT[14]
 (defn ^:no-doc replace-repeated-seqs-parens1
   [s kind]
@@ -318,6 +332,7 @@
    remove-alternative
    remove-inv-bases
    remove-del-count-from-delins
+   replace-unknown-repeated-seq
    replace-repeated-seqs-parens1
    replace-repeated-seqs-parens2
    remove-genomic-bases-from-protein

diff --git a/test/clj_hgvs/core_test.cljc b/test/clj_hgvs/core_test.cljc
@@ -332,6 +332,11 @@
     ;; remove-del-count-from-delins
     "c.123_124del2insCTGA" "c.123_124delinsCTGA"
 
+    ;; replace-unknown-repeated-seq
+    "g.1134_1135ins(100)" "g.1134_1135insN[100]"
+    "r.431_432ins(5)"     "r.431_432insn[5]"
+    "p.R78_G79ins23"      "p.R78_G79insX[23]"
+
     ;; replace-repeated-seqs-parens1
     "c.112GAT(14)" "c.112GAT[14]"