de8dff345414

--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/src/problems/corr.lisp	Tue Dec 14 19:11:27 2021 -0500
@@ -0,0 +1,61 @@
+(defpackage :rosalind/corr (:use :cl :rosalind :losh :iterate))
+(in-package :rosalind/corr)
+
+(defparameter *input*
+  ">Rosalind_52
+TCATC
+>Rosalind_44
+TTCAT
+>Rosalind_68
+TCATC
+>Rosalind_28
+TGAAA
+>Rosalind_95
+GAGGA
+>Rosalind_66
+TTTCA
+>Rosalind_33
+ATCAA
+>Rosalind_21
+TTGAT
+>Rosalind_18
+TTTCC
+")
+
+(defparameter *output*
+  "GAGGA->GATGA
+TTCAT->TTGAT
+TTTCC->TTTCA
+")
+
+
+;;;; Problem ------------------------------------------------------------------
+(defun read-frequencies (reads)
+  (iterate
+    (with result = (make-hash-table :test #'equal))
+    (for read :in reads)
+    (incf (gethash read result 0))
+    (for read-rc = (u:reverse-complement read))
+    (unless (string= read read-rc)
+      (incf (gethash read-rc result 0)))
+    (returning (remhash-if-value (curry #'= 1) result))))
+
+(defun find-correction (read freqs)
+  (iterate (for (good nil) :in-hashtable freqs)
+           (finding good :such-that (= 1 (u:hamming good read)))))
+
+(define-problem corr (data stream) *input* *output*
+  (iterate
+    (with reads = (mapcar #'cdr (u:read-fasta-into-alist data)))
+    (with freqs = (read-frequencies reads))
+    (for r :in reads)
+    (unless (gethash r freqs)
+      (collect (format nil "~A->~A" r (find-correction r freqs)) :into result))
+    (returning (str:join #\newline (sort result #'string<))))) ; sort for test
+
+
+#; Scratch --------------------------------------------------------------------
+
+(problem-corr)
+
+(time (solve corr))