src/problems/sseq.lisp @ 64aa58880d55
EVAL
author |
Steve Losh <steve@stevelosh.com> |
date |
Sat, 23 Feb 2019 12:42:13 -0500 |
parents |
e0c558fa549b |
children |
2735aa6aab79 |
(in-package :rosalind)
(defparameter *input-sseq* ">Rosalind_14
ACGTACGTGACG
>Rosalind_18
GTA
")
(defparameter *output-sseq* "3 4 5")
;; todo: make this more efficient for lists
(defun subsequence-positions (needle haystack &key
(test #'eql)
(start-needle 0)
(end-needle (length needle))
(start-haystack 0)
(end-haystack (length haystack)))
(iterate
(with ni = start-needle)
(with n = (elt needle ni))
(for h :in-vector haystack :with-index hi :from start-haystack :below end-haystack)
(when (funcall test n h)
(collect hi :into result)
(incf ni)
(if (= ni end-needle)
(return result)
(setf n (elt needle ni))))))
(define-problem sseq (data stream)
*input-sseq*
*output-sseq*
(let* ((haystack (nth-value 1 (read-fasta data)))
(needle (nth-value 1 (read-fasta data))))
(-<> (subsequence-positions needle haystack :test #'char=)
(mapcar #'1+ <>)
(format nil "~{~D~^ ~}" <>))))