temp.clj

(defn viterbi [qs es ks xs]
  (clojure.pprint/pprint "Hello world")
  (let [initial-ctx {:qs qs, :es es, :pis-prev {["*" "*"] 1.0}, :bps []}
        ks-adder (fn [idx x] (case idx
                               0 [x #{"*"} #{"*"} ks]
                               1 [x #{"*"} ks ks]
                               [x ks ks ks]))
        xs-and-ks (into [] (map-indexed ks-adder xs))
        {:keys [bps pis-prev]} (reduce viterbi-folder initial-ctx xs-and-ks)
        [[_ y-last :as ys-tail] _] (argmax-max (fn [[u v]] (* (pis-prev [u v])
                                                              (qs ["STOP" u v])))
                                               (for [u ks v ks] [u v]))
        backtrack (->> (reductions (fn [[y1 y2 :as t] bt] [(bt t) y1])
                                   ys-tail (rseq bps))
                       (map first)
                       (cons y-last)
                       (reverse)
                       (drop 2)
                       (into []))]
    backtrack))

(defn part2-tag [file-in file-out]
  (let [{wordtags Wordtag,
         two-grams Two-gram,
         three-grams Three-gram} (read-grouped-data rared-counts-file)
        tag-counts (count-tags wordtags)
        word-counts (count-words wordtags)
        es (get-es wordtags tag-counts)
        qs (get-qs three-grams two-grams)
        tagged-file (for [sentence (clojure.string/split (slurp file-in)
                                                         #"\n\n")
                          :let [
                                words (clojure.string/split-lines sentence)
                                rared (map #(if (< (or (word-counts %) 0) 5)
                                              "_RARE_" %)
                                           words)
                                xs (conj (into [] rared) "STOP")
                                tags (viterbi qs es #{"I-GENE" "O"} xs) ;; CAUSES NPE WHEN UNCOMMENTED WITHOUT DEBUG PPRINTING
                                ]]
                      (do (clojure.pprint/pprint (take 3 xs))
                          xs)
                      ;; tags

                      )]
    #_(spit file-out (str (clojure.string/join "\n" tagged-file) "\n"))
    tagged-file))