src/problems/kmer.lisp @ 2d34585c5704
Clean up, remove quickutils
author |
Steve Losh <steve@stevelosh.com> |
date |
Sun, 19 Jan 2020 19:51:35 -0500 |
parents |
e0c558fa549b |
children |
2735aa6aab79 |
(in-package :rosalind)
(defparameter *input-kmer* ">Rosalind_6431
CTTCGAAAGTTTGGGCCGAGTCTTACAGTCGGTCTTGAAGCAAAGTAACGAACTCCACGG
CCCTGACTACCGAACCAGTTGTGAGTACTCAACTGGGTGAGAGTGCAGTCCCTATTGAGT
TTCCGAGACTCACCGGGATTTTCGATCCAGCCTCAGTCCAGTCTTGTGGCCAACTCACCA
AATGACGTTGGAATATCCCTGTCTAGCTCACGCAGTACTTAGTAAGAGGTCGCTGCAGCG
GGGCAAGGAGATCGGAAAATGTGCTCTATATGCGACTAAAGCTCCTAACTTACACGTAGA
CTTGCCCGTGTTAAAAACTCGGCTCACATGCTGTCTGCGGCTGGCTGTATACAGTATCTA
CCTAATACCCTTCAGTTCGCCGCACAAAAGCTGGGAGTTACCGCGGAAATCACAG")
(defparameter *output-kmer* "4 1 4 3 0 1 1 5 1 3 1 2 2 1 2 0 1 1 3 1 2 1 3 1 1 1 1 2 2 5 1 3 0 2 2 1 1 1 1 3 1 0 0 1 5 5 1 5 0 2 0 2 1 2 1 1 1 2 0 1 0 0 1 1 3 2 1 0 3 2 3 0 0 2 0 8 0 0 1 0 2 1 3 0 0 0 1 4 3 2 1 1 3 1 2 1 3 1 2 1 2 1 1 1 2 3 2 1 1 0 1 1 3 2 1 2 6 2 1 1 1 2 3 3 3 2 3 0 3 2 1 1 0 0 1 4 3 0 1 5 0 2 0 1 2 1 3 0 1 2 2 1 1 0 3 0 0 4 5 0 3 0 2 1 1 3 0 3 2 2 1 1 0 2 1 0 2 2 1 2 0 2 2 5 2 2 1 1 2 1 2 2 2 2 1 1 3 4 0 2 1 1 0 1 2 2 1 1 1 5 2 0 3 2 1 1 2 2 3 0 3 0 1 3 1 2 3 0 2 1 2 2 1 2 3 0 1 2 3 1 1 3 1 0 1 1 3 0 2 1 2 2 0 2 1 1")
(defun mapc-kmers (function n &key (copy t))
(let ((kmer (make-array n :element-type 'character)))
(recursively ((i 0))
(if (= i n)
(funcall function (if copy
(copy-seq kmer)
kmer))
(flet ((branch (base)
(setf (aref kmer i) base)
(recur (1+ i))))
(map nil #'branch "ACGT"))))))
(defun map-kmers (function n)
(gathering (mapc-kmers (compose #'gather function) n)))
(defun kmers (n)
(map-kmers #'identity n))
(define-problem kmer (data stream)
*input-kmer*
*output-kmer*
(iterate
(with n = 4)
(with seq = (nth-value 1 (read-fasta data)))
(with counts = (make-hash-table :test #'equal))
(for i :from 0 :to (- (length seq) n))
(for kmer = (subseq seq i (+ i n)))
(incf (gethash kmer counts 0))
(finally
(return
(format nil "~{~D~^ ~}"
(map-kmers (lambda (kmer) (gethash kmer counts 0)) n))))))