1b97142d9722

MOTZ
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author Steve Losh <steve@stevelosh.com>
date Sat, 30 Apr 2022 21:11:44 -0400
parents 6aa19c08b5cf
children 5616829c5d4f
branches/tags (none)
files src/problems/motz.lisp

Changes

diff -r 6aa19c08b5cf -r 1b97142d9722 src/problems/motz.lisp
--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/problems/motz.lisp	Sat Apr 30 21:11:44 2022 -0400
@@ -0,0 +1,49 @@
+(defpackage :rosalind/motz (:use :cl :rosalind :losh :iterate))
+(in-package :rosalind/motz)
+
+(defparameter *input*
+  ">Rosalind_57
+AUAU")
+
+(defparameter *output*
+  "2")
+
+
+;;;; Problem ------------------------------------------------------------------
+(defun rna-bases-pair-p (base1 base2)
+  (char= base1 (ecase base2
+                 (#\A #\U)
+                 (#\U #\A)
+                 (#\G #\C)
+                 (#\C #\G))))
+
+(defun rna-matches (rna &aux (cache (make-hash-table)))
+  (recursively ((start 0)
+                (end (length rna)))
+    (if (= start end)
+      1
+      (alexandria:ensure-gethash (complex start end) cache
+        (+ (recur (1+ start) end)
+           (iterate
+             ;; Arbitrarily pick char 0 as one of the ends of the match to avoid
+             ;; needing to cross the end of the RNA sequence when recurring.
+             (with b1 = (char rna start))
+             ;; Unlike CAT, for MOTZ we allow odd-length subsequences.
+             (for b2 :in-string rna :from (1+ start) :below end :with-index i)
+             (when (rna-bases-pair-p b1 b2)
+               (summing (* (recur (1+ start) i)
+                           (recur (1+ i) end))))))))))
+
+(define-problem motz (data stream) *input* *output*
+  (mod (rna-matches (nth-value 1 (u:read-fasta data))) 1000000))
+
+
+#; Scratch --------------------------------------------------------------------
+
+
+(problem-motz)
+
+(problem-motz "UAGCGUGAUCAC")
+
+(time (solve motz))
+