src/problems/prob.lisp @ 9b2cfb112dd6

(in-package :rosalind)

(defparameter *input-prob*
  "ACGATACAA
0.129 0.287 0.423 0.476 0.641 0.742 0.783")

(defparameter *output-prob*
  "-5.737 -5.217 -5.263 -5.360 -5.958 -6.628 -7.009")


(define-problem prob (data stream)
    *input-prob*
    *output-prob*
  (let ((dna (read-line data))
        (gc-contents (read-all-from-string (read-line data))))
    (labels
        ((gcp (base)
           "Return whether `base` is G or C."
           (or (char= #\G base)
               (char= #\C base)))
         (base-probability (gc-content base)
           "Return the probability of `base` in DNA with the given `gc-content`."
           (if (gcp base)
             (/ gc-content 2)
             (/ (- 1 gc-content) 2)))
         (prob (gc-content)
           (iterate
             (for base :in-string dna)
             (summing (log (base-probability gc-content base) 10)))))
      (format nil "~{~,3F~^ ~}" (mapcar #'prob gc-contents)))))