Merge pull request #116 from chrovis/fix/fix-around-ter-codon-protein-variant

Author: federkasten

src/varity/vcf_to_hgvs/protein.clj

@@ -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
@@ -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
@@ -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)
 

test/varity/vcf_to_hgvs_test.clj

@@ -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 (+)
@@ -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