return no-effect when ter site is inserted around ter site

Author: nokara26

src/varity/vcf_to_hgvs/protein.clj

@@ -179,8 +179,11 @@
 
 (defn- ter-site-same-pos?
   [ref-prot-seq alt-prot-seq]
-  (let [ter-site-pos (dec (count ref-prot-seq))]
-    (= \* (get alt-prot-seq ter-site-pos))))
+  (let [ref-ter-pos (count ref-prot-seq)
+        alt-ter-pos (inc (count (first (string/split alt-prot-seq #"\*"))))]
+    (and (string/includes? ref-prot-seq "*")
+         (string/includes? alt-prot-seq "*")
+         (= ref-ter-pos alt-ter-pos))))
 
 (defn- cds-start-upstream?
   [cds-start pos ref alt]
@@ -443,7 +446,9 @@
 
                                            :else
                                            :frame-shift)
-              (and (pos? npref) (= (first palt-only) \*)) :substitution
+              (and (pos? npref) (= (first palt-only) \*)) (if (ter-site-same-pos? ref-prot-seq alt-prot-seq*)
+                                                            :no-effect
+                                                            :substitution)
               (not= ref-prot-rest alt-prot-rest) (cond
                                                    (or (and (= (first alt-prot-rest) \*)
                                                             (>= nprefo npalto)
@@ -572,45 +577,45 @@
                                      (coord/unknown-coordinate))))))))
 
 (defn- protein-extension
-  [ppos pref palt {:keys [ref-prot-seq alt-tx-prot-seq c-ter-adjusted-alt-prot-seq ini-offset prefer-extension-for-initial-codon-alt?] :as seq-info}]
-  (cond
-    (and (not= ppos 1)
-         (ter-site-same-pos? ref-prot-seq c-ter-adjusted-alt-prot-seq))
-    (mut/protein-no-effect)
+  [ppos pref palt {:keys [ref-prot-seq alt-tx-prot-seq ini-offset prefer-extension-for-initial-codon-alt?] :as seq-info}]
+  (let [alt-prot-seq* (format-alt-prot-seq seq-info)]
+    (cond
+      (and (not= ppos 1)
+           (ter-site-same-pos? ref-prot-seq alt-prot-seq*))
+      (mut/protein-no-effect)
 
-    (and (= ppos 1) (not prefer-extension-for-initial-codon-alt?))
-    (mut/protein-unknown-mutation)
+      (and (= ppos 1) (not prefer-extension-for-initial-codon-alt?))
+      (mut/protein-unknown-mutation)
 
-    :else
-    (let [[_ ins offset _] (diff-bases (or pref "") (or palt ""))
-          alt-prot-seq* (format-alt-prot-seq seq-info)
-          ini-site ((comp str first) ref-prot-seq)
-          first-diff-aa-info (if (= ppos 1)
-                               {:ppos 1
-                                :pref ini-site}
-                               (get-first-diff-aa-info ppos
-                                                       ref-prot-seq
-                                                       alt-prot-seq*))
-          rest-seq (if (= ppos 1)
-                     (-> alt-tx-prot-seq
-                         (subs 0 ini-offset)
-                         reverse
-                         (#(apply str %)))
-                     (subs alt-prot-seq* (:ppos first-diff-aa-info)))
-          alt-aa (mut/->long-amino-acid (if (= ppos 1)
-                                          (or (last ins) (first rest-seq))
-                                          (:palt first-diff-aa-info)))
-          alt-aa-offset (if (and (= ppos 1) (nil? (last ins))) -1 0)
-          new-aa-pos (some-> (string/index-of rest-seq (:pref first-diff-aa-info)) inc (+ alt-aa-offset))]
-      (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)))
-                               alt-aa
-                               (if (= ppos 1) :upstream :downstream)
-                               (if new-aa-pos
-                                 (coord/protein-coordinate new-aa-pos)
-                                 (coord/unknown-coordinate)))))))
+      :else
+      (let [[_ ins offset _] (diff-bases (or pref "") (or palt ""))
+            ini-site ((comp str first) ref-prot-seq)
+            first-diff-aa-info (if (= ppos 1)
+                                 {:ppos 1
+                                  :pref ini-site}
+                                 (get-first-diff-aa-info ppos
+                                                         ref-prot-seq
+                                                         alt-prot-seq*))
+            rest-seq (if (= ppos 1)
+                       (-> alt-tx-prot-seq
+                           (subs 0 ini-offset)
+                           reverse
+                           (#(apply str %)))
+                       (subs alt-prot-seq* (:ppos first-diff-aa-info)))
+            alt-aa (mut/->long-amino-acid (if (= ppos 1)
+                                            (or (last ins) (first rest-seq))
+                                            (:palt first-diff-aa-info)))
+            alt-aa-offset (if (and (= ppos 1) (nil? (last ins))) -1 0)
+            new-aa-pos (some-> (string/index-of rest-seq (:pref first-diff-aa-info)) inc (+ alt-aa-offset))]
+        (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)))
+                                 alt-aa
+                                 (if (= ppos 1) :upstream :downstream)
+                                 (if new-aa-pos
+                                   (coord/protein-coordinate new-aa-pos)
+                                   (coord/unknown-coordinate))))))))
 
 (defn- protein-indel
   [ppos pref palt {:keys [ref-prot-seq c-ter-adjusted-alt-prot-seq

test/varity/vcf_to_hgvs_test.clj

@@ -301,6 +301,7 @@
         "chr11" 14279340 "G" "A" '("p.=") ; not actual example (-)
         "chr7" 55019277 "G" "GTC" '("p.=") ; not actual example (+)
         "chr17" 21042835 "T" "TG" '("p.=") ; not actual example (-)
+        "chr13" 24421121 "A" "ATTA" '("p.=") ; not actual example (-)
 
         ;; unknown
         "chr12" 40393453 "G" "A" '("p.?") ; not actual example (+)