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Fix around ter codon variant #116

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merged 2 commits into from
Jan 28, 2025
Merged

Fix around ter codon variant #116

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c161a91
fix: add substitution condition to delins
nokara26 Jan 27, 2025
ceeedf9
fix: fix termination codon position in extension
nokara26 Jan 27, 2025
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7 changes: 5 additions & 2 deletions src/varity/vcf_to_hgvs/protein.clj
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Original file line number Diff line number Diff line change
Expand Up @@ -590,7 +590,7 @@
(mut/protein-unknown-mutation)

:else
(let [[_ ins offset _] (diff-bases (or pref "") (or palt ""))
(let [[_ ins _ _] (diff-bases (or pref "") (or palt ""))
ini-site ((comp str first) ref-prot-seq)
first-diff-aa-info (if (= ppos 1)
{:ppos 1
Expand All @@ -612,7 +612,7 @@
(if (and (= ppos 1) (= alt-aa "Ter"))
(mut/protein-unknown-mutation)
(mut/protein-extension (if (= ppos 1) (mut/->long-amino-acid ini-site) "Ter")
(coord/protein-coordinate (if (= ppos 1) 1 (+ ppos offset)))
(coord/protein-coordinate (if (= ppos 1) 1 (:ppos first-diff-aa-info)))
alt-aa
(if (= ppos 1) :upstream :downstream)
(if new-aa-pos
Expand Down Expand Up @@ -650,6 +650,9 @@
(every? empty? [del ins])
(mut/protein-no-effect)

(= 1 (count del) (count ins))
(protein-substitution ppos* pref* palt* seq-info)

(empty? del)
(protein-insertion ppos* pref* palt* seq-info)

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2 changes: 2 additions & 0 deletions test/varity/vcf_to_hgvs_test.clj
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Original file line number Diff line number Diff line change
Expand Up @@ -201,6 +201,7 @@
"chr17" 31159027 "TGC" "T" '("p.A75*") ; not actual example (+, nonsense in del case)
"chr2" 47478341 "TG" "T" '("p.L762*" "p.L696*") ;; rs786204050 (+) frameshift with termination
"chr17" 7676202 "T" "TGTCCCTTAGTCTT" '("p.P58*" "p.P19*") ; cf. not actual example (-, frameshift with termination)
"chr13" 24421115 "TGACTTAGCC" "T" '("p.G1724K") ; not actual example (-, del includes termination codon)

;; deletion
"chr1" 240092288 "AGTC" "A" '("p.S61del") ; cf. rs772088733 (+)
Expand Down Expand Up @@ -282,6 +283,7 @@
"chr10" 87965468 "TC" "T" '("p.*404Eext*11" "p.*577Eext*11" "p.*207Eext*11") ; not actual example (+)
"chrX" 15823239 "ATAA" "A" '("p.*483Text*?") ; not actual example (+)
"chr13" 24421118 "CTTA" "C" '("p.*1725Vext*2") ; not actual example (-)
"chrX" 15823235 "CCAAA" "C" '("p.*483Lext*?") ; not actual example (+)
;; NOTE: There are very few correct examples...

;; Extension without termination site
Expand Down
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