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(defn join-sto-fasta-lines [infilespec origin]
  (let [[seq-lines gc-lines] (sto-GC-and-seq-lines infilespec)
        
        gc-lines (if (not= origin "")
                   (concat (take 1 gc-lines) [origin] (drop 1 gc-lines))
                   gc-lines)
        recombined-seqs (sort-by
                         #(-> % second first)
                         (vec
                          (reduce

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#!/usr/bin/perl
my $p = 'AAMAAT-ATAMAAAT-AT'; #example protein
my @l = find_orfs($p);        #calls subfunction
my ($longest, $longest_aa) = longest_orf($p, @l); #calls subfunction
print "protein = $longest_aa longest = $longest\n";

sub find_orfs ($protein) {
  my ($protein) = @_;
  print "protein $protein\n";
  my $len = length ($protein);

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(ns smith-waterman)

(defn- array-keys
  "positions of the array to work on"

  [s1 s2]
  (for [i (range (count s1)) ;initialize scoring array. similar to a sparse matrix
        j (range (count s2))]
    [i j]))

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(let [[nm sq] (cond
                                            (.startsWith l "#=GC SS_cons")
                                            [(str/join " " (butlast (str/split #"\s+" l))) (last (str/split #"\s+" l))] ;;splits the line apart and hopefully creates vector  ["#GC SS_cons" structure]
                                            (.startsWith l "#")
                                            (str/split #"\s{2,}+" l)
                                            :else
                                            (str/split #"\s+" l))
                                   prev (get m nm [(gen-uid) ""])]
                               (assoc m  nm [(first prev)
                                             (str (second prev) sq)]))

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(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)))]])

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(defn nussinov
  "Uses the Nussinov algorithm to compute an optimal RNA structure by
  maximizing base pairs in the structure. The function requires an
  input string s. The output is a list of base pair locations [i
  j]. It will also print out the sequence and the structure so that it
  can be visually inspected. An example sequence of 'GGGAAAUCC' will
  give the answer ([2 6] [1 7] [0 8]). Locations are 0 based (ie seq
  goes from 0 to n-1)."
  
  [s]

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;;; init.el --- Where all the magic begins
;;
;; Part of the Emacs Starter Kit
;;
;; This is the first thing to get loaded.
;;
;; "Emacs outshines all other editing software in approximately the
;; same way that the noonday sun does the stars. It is not just bigger
;; and brighter; it simply makes everything else vanish."
;; -Neal Stephenson, "In the Beginning was the Command Line"

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(ns sudoku
  (:require [clojure.contrib.io :as io]
            [clojure.contrib.string :as str]
            [clojure.set :as sets]))

;;;example input for testing
(def grid01
  (list "003020600"
        "900305001"
        "001806400"

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(require '[clojure.java.jdbc :as jdbc]
         '[korma.db :as kdb]
         '[korma.core :as kcore]
         '[sqlingvo.core :as sql]
         '[sqlingvo.vendor :as v]))

;;;examples here are directly from the sqlingvo, jdbc, korma websites
;;;in order to provide a concrete example of using a SQL DSL with jdbc
;;;to execute mysql commands

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(ns mysql-test
  (:require [clojure.java.jdbc :as jdbc])
  (:use [edu.bc.bio.sequtils.files]))




(def mysql-ds
  {:classname "com.mysql.jdbc.Driver"
   :subprotocol "mysql"