revcomp.clj

(ns user)

(defn- reverse-base [base]
  (let [mapping { :A \T :T \A :G \C :C \G }
        key     (keyword (.toString base))]
    (key mapping)))

(defn reverse-complement [sequence]
  (let [rev-seq (reverse (.toUpperCase sequence))]
    (map reverse-base rev-seq)))

(println "Reverse complement gives" (reverse-complement "TGAC"))

Nice. My version reads like (println "Revcomp:" (reverse-str (complement "TGAC")))

My problem: how to use a "bio" namespace here? The "complement" function is already defined in clojure/core, so gives issues. Am trying to do something like (ns bio), but then it can't find "defn" anymore...

can't def complement because namespace: bio refers to:#'clojure.core/complement

jan.

You might be able to use something like the following to exclude 'complement' from the namespace:

http://stackoverflow.com/questions/2832582/how-to-rename-an-operation-in-clojure/2834069#2834069

(That example excludes + but the principle should be the same)

To be honest though, I'm not sure... Namespaces are the one major thing in clojure which don't currently fit in my brain (which comes from C, Java and Groovy which all seem to follow the same or similar forms) :-(

Thanks for that link. Does help to clear it up at least a little bit for me. Trouble is that the core 'complement' cannot be easily accessed then (apart from prepending "clojure.core/"). Would be nice if we could say:
(println bio/complement(bio/reverse-str "TGACC"))
i.e. adding "bio" in front.

@wmacgyver: This is the code that we're trying to get going:

  (ns bio)
  (defn reverse-str
    "Reverse a string"
    [s]
    (apply str (reverse s))
  )
  
  (defn complement
    "Complement a base"
    [base]
    (let [mapping { :A \T :T \A :G \C :C \G }
      key (keyword (.toString base))]
      (key mapping)))
  )
  
  (println bio/complement (bio/reverse-str "TGACC"))

Output should be: "GGTCA"