src/problems/prot.lisp @ e279056b1a5b
Start taking some notes
author |
Steve Losh <steve@stevelosh.com> |
date |
Sat, 03 Nov 2018 18:20:48 -0400 |
parents |
8de2e6d7c9d9 |
children |
b3598dc7ef5c |
(in-package :rosalind)
(defmacro codon-case ((vector index) &rest clauses)
;; Compiles a giant list of clauses into a tree of ECASEs.
;;
;; Each codon will have at most 3 ECASEs to pass through. Each ECASE has at
;; most four options, so in the worst case we end up with 3 * 4 = 12
;; comparisons instead of 64.
;;
;; If we ever convert bases to vectors of (unsigned-byte 2)s we could
;; potentially use a lookup table here, e.g.:
;;
;; (aref +amino-acids+ (+ x (ash y 2) (ash z 4)))
(alexandria:once-only (vector index)
(alexandria:with-gensyms (x y z)
`(let ((,x (aref ,vector ,index))
(,y (aref ,vector (+ ,index 1)))
(,z (aref ,vector (+ ,index 2))))
,(labels ((strip (clauses)
(if (= 1 (length (caar clauses)))
(cadar clauses)
(iterate (for (head body) :in clauses)
(collect (list (subseq head 1) body)))))
(split (clauses)
(-<> clauses
(group-by (rcurry #'aref 0) <> :key #'first)
(iterate (for (k v) :in-hashtable <>)
(collect (list k (strip v)))))))
(recursively ((clauses (split clauses))
(codons (list x y z))
(i 0))
`(ecase ,(first codons)
,@(iterate (for (k remaining) :in clauses)
(collect `(,k ,(if (atom remaining)
remaining
(recur (split remaining)
(rest codons)
(1+ i)))))))))))))
(defun codon-to-protein (vector index)
"Return the amino acid encoded by the codon in `vector` at `index`."
(codon-case (vector index)
("UUU" #\F) ("CUU" #\L) ("AUU" #\I) ("GUU" #\V)
("UUC" #\F) ("CUC" #\L) ("AUC" #\I) ("GUC" #\V)
("UUA" #\L) ("CUA" #\L) ("AUA" #\I) ("GUA" #\V)
("UUG" #\L) ("CUG" #\L) ("AUG" #\M) ("GUG" #\V)
("UCU" #\S) ("CCU" #\P) ("ACU" #\T) ("GCU" #\A)
("UCC" #\S) ("CCC" #\P) ("ACC" #\T) ("GCC" #\A)
("UCA" #\S) ("CCA" #\P) ("ACA" #\T) ("GCA" #\A)
("UCG" #\S) ("CCG" #\P) ("ACG" #\T) ("GCG" #\A)
("UAU" #\Y) ("CAU" #\H) ("AAU" #\N) ("GAU" #\D)
("UAC" #\Y) ("CAC" #\H) ("AAC" #\N) ("GAC" #\D)
("UAA" nil) ("CAA" #\Q) ("AAA" #\K) ("GAA" #\E)
("UAG" nil) ("CAG" #\Q) ("AAG" #\K) ("GAG" #\E)
("UGU" #\C) ("CGU" #\R) ("AGU" #\S) ("GGU" #\G)
("UGC" #\C) ("CGC" #\R) ("AGC" #\S) ("GGC" #\G)
("UGA" nil) ("CGA" #\R) ("AGA" #\R) ("GGA" #\G)
("UGG" #\W) ("CGG" #\R) ("AGG" #\R) ("GGG" #\G)))
(defun translate (rna &key (start 0))
"Translate a string of RNA bases into a protein string of amino acids."
(iterate (for i :from (search "AUG" rna :start2 start) :by 3)
(for protein = (codon-to-protein rna i))
(while protein)
(collect protein :result-type 'string)))
(define-problem prot (data string)
"AUGGCCAUGGCGCCCAGAACUGAGAUCAAUAGUACCCGUAUUAACGGGUGA"
"MAMAPRTEINSTRING"
(translate data))
;; (solve prot)