src/problems/sseq.lisp @ 97dda08645b3
default tip
SCSP
author |
Steve Losh <steve@stevelosh.com> |
date |
Mon, 08 Aug 2022 19:26:18 -0400 |
parents |
86d92162dc1f |
children |
(none) |
(defpackage :rosalind/sseq (:use :cl :rosalind :losh :iterate))
(in-package :rosalind/sseq)
(defparameter *input* ">Rosalind_14
ACGTACGTGACG
>Rosalind_18
GTA
")
(defparameter *output* "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* *output*
(let* ((haystack (nth-value 1 (u:read-fasta data)))
(needle (nth-value 1 (u:read-fasta data))))
(_ (subsequence-positions needle haystack :test #'char=)
(mapcar #'1+ _)
(format nil "~{~D~^ ~}" _))))