convert a stockholm file to clustal w format.

gistfile1.clj

(defn sto->aln
  "Convert a stockhom format alignment file into its ClustalW
   equivalent ALN format.  STOIN is the filespec for the stockholm
   format file and ALNOUT is the filespec for the resulting
   conversion (it is overwritten if it already exists!)"

  [stoin alnout]
  (let [seq-lines (second (join-sto-fasta-lines stoin ""))
        seq-lines (map (fn [[nm [uid sl]]]
                         [nm [uid (map #(str/join "" %) (partition-all 60 (str/replace-re #"\." "-" sl)))]])
                       seq-lines)]
    (io/with-out-writer alnout
      (println "CLUSTAL W (1.83) multiple sequence alignment\n")
      (loop [x seq-lines]
        (let [[nm [uid sl]] (first x)]
          (when (not-empty sl)
            (do 
              (doseq [[nm [uid sl]] x]
                (cl-format true "~A~40T~A~%" nm (first sl)))
              (println "")
              (recur (map (fn [[nm [uid sl]]]
                            [nm [uid (rest sl)]])
                          x)))))))
    alnout)

  ;; (let [seq-lines (filter #(not (or (= "//" %) (re-find #"^#" %)))
  ;;                         (first (sto-GC-and-seq-lines stoin)))
  ;;       seq-lines (map #(str/replace-re #"\." "-" %) seq-lines)]
  ;;   (io/with-out-writer (fs/fullpath alnout)
  ;;     (println "CLUSTAL W (1.83) multiple sequence alignment\n")
  ;;     (doseq [sl seq-lines]
  ;;       (println sl)))
  ;;   alnout)
  )