Initial data commit

Task/Bioinformatics-base-count/Racket/bioinformatics-base-count.rkt

@@ -0,0 +1,55 @@
+#lang racket
+
+(define (fold-sequence seq kons #:finalise (finalise (λ x (apply values x))) . k0s)
+  (define (recur seq . ks)
+    (if (null? seq)
+      (call-with-values (λ () (apply finalise ks)) (λ vs (apply values vs)))
+      (call-with-values (λ () (apply kons (car seq) ks)) (λ ks+ (apply recur (cdr seq) ks+)))))
+  (apply recur (if (string? seq) (string->list (regexp-replace* #px"[^ACGT]" seq "")) seq) k0s))
+
+(define (sequence->pretty-printed-string seq)
+  (define (fmt idx cs-rev) (format "~a: ~a" (~a idx #:width 3 #:align 'right) (list->string (reverse cs-rev))))
+  (fold-sequence
+    seq
+    (λ (b n start-idx lns-rev cs-rev)
+       (if (zero? (modulo n 50))
+	 (values (+ n 1) n (if (pair? cs-rev) (cons (fmt start-idx cs-rev) lns-rev) lns-rev) (cons b null))
+	 (values (+ n 1) start-idx lns-rev (cons b cs-rev))))
+    0 0 null null
+    #:finalise (λ (n idx lns-rev cs-rev)
+		(string-join (reverse (if (null? cs-rev) lns-rev (cons (fmt idx cs-rev) lns-rev))) "\n"))))
+
+(define (count-bases b as cs gs ts n)
+  (values (+ as (if (eq? b #\A) 1 0))
+	  (+ cs (if (eq? b #\C) 1 0))
+	  (+ gs (if (eq? b #\T) 1 0))
+	  (+ ts (if (eq? b #\G) 1 0))
+	  (add1 n)))
+
+(define (bioinformatics-Base_count s)
+  (define-values (as cs gs ts n) (fold-sequence s count-bases 0 0 0 0 0))
+  (printf "SEQUENCE:~%~%~a~%~%" (sequence->pretty-printed-string s))
+  (printf "BASE COUNT:~%-----------~%~%~a~%~%"
+	  (string-join (map (λ (c n) (format " ~a :~a" c (~a #:width 4 #:align 'right n)))
+			    '(A T C G)
+			    (list as ts cs gs)) "\n"))
+  (newline)
+  (printf "TOTAL: ~a~%" n))
+
+(module+
+  main
+  (define the-string
+    #<<EOS
+CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
+CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
+AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
+GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
+CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
+TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
+TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT
+CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
+TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC
+GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT
+EOS
+)
+  (bioinformatics-Base_count the-string))