feat: add fn that returns exon/intron region of the given pos

Author: nokara26

src/varity/ref_gene.clj

@@ -526,3 +526,25 @@
         :else
         (throw (ex-info "The coordinate is invalid for the refGene."
                         {:type ::invalid-coordinate, :coordinate coord}))))))
+
+(defn- ranges->regions
+  [ranges region strand]
+  (let [ranges (if (= strand :forward)
+                 ranges
+                 (reverse ranges))]
+    (map-indexed (fn [idx range] {:range range
+                                  :region region
+                                  :index (inc idx)
+                                  :length (count ranges)})
+                 ranges)))
+
+(defn pos->region
+  "Returns exon or intron region of the given position"
+  [pos {:keys [strand exon-ranges]}]
+  (let [intron-ranges (exon-ranges->intron-ranges exon-ranges)
+        regions (concat (ranges->regions exon-ranges "exon" strand)
+                        (ranges->regions intron-ranges "intron" strand))
+        include-pos? (fn [{:keys [range]}]
+                       (let [[s e] range]
+                         (<= s pos e)))]
+    (first (filter include-pos? regions))))

test/varity/ref_gene_test.clj

@@ -544,3 +544,27 @@
       "5+1" :reverse
       "4-1" :reverse
       "3+1" :reverse)))
+
+(deftest ranges->regions-test
+  (let [ranges [[10 20] [30 40] [50 60]]]
+    (is (= (#'rg/ranges->regions ranges "exon" :forward)
+           [{:range [10 20] :region "exon" :index 1 :length 3}
+            {:range [30 40] :region "exon" :index 2 :length 3}
+            {:range [50 60] :region "exon" :index 3 :length 3}]))
+    (is (= (#'rg/ranges->regions ranges "exon" :reverse)
+           [{:range [50 60] :region "exon" :index 1 :length 3}
+            {:range [30 40] :region "exon" :index 2 :length 3}
+            {:range [10 20] :region "exon" :index 3 :length 3}]))))
+
+(deftest pos->region
+  (let [ranges [[10 20] [30 40] [50 60]]]
+    (testing "forward"
+      (are [pos pred] (= (rg/pos->region pos {:strand :forward :exon-ranges ranges})
+                         pred)
+        10 {:range [10 20] :region "exon" :index 1 :length 3}
+        25 {:range [21 29] :region "intron" :index 1 :length 2}))
+    (testing "reverse"
+      (are [pos pred] (= (rg/pos->region pos {:strand :reverse :exon-ranges ranges})
+                         pred)
+        10 {:range [10 20] :region "exon" :index 3 :length 3}
+        25 {:range [21 29] :region "intron" :index 2 :length 2}))))