Bioinformatics/base count

From Rosetta Code
Revision as of 21:16, 26 November 2019 by Hout (talk | contribs) (→‎{{header|Python}}: Added a functional variant, using the GenBank format.)
Bioinformatics/base count is a draft programming task. It is not yet considered ready to be promoted as a complete task, for reasons that should be found in its talk page.

Given this string representing ordered DNA bases: 

CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT
CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC
GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT
  1. "Pretty print" the sequence followed by a summary of the counts of each of the bases, (A, C, G, and T) in the sequence as well as the total count of bases in the string.



Factor

<lang factor>USING: assocs formatting grouping io kernel literals math math.statistics prettyprint qw sequences sorting ;

CONSTANT: dna $[ 

   qw{
       CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
       CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
       AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
       GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
       CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
       TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
       TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT
       CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
       TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC
       GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT
   } concat

]

.dna ( seq n -- )
   "SEQUENCE:" print [ group ] [ ] bi
   [ * swap "  %3d: %s\n" printf ] curry each-index ;
show-counts ( seq -- )
   "BASE COUNTS:" print histogram >alist [ first ] sort-with
   [ [ "    %c: %3d\n" printf ] assoc-each ]
   [ "TOTAL: " write [ second ] [ + ] map-reduce . ] bi ;

dna [ 50 .dna nl ] [ show-counts ] bi</lang>

Output:
SEQUENCE:
    0: CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
   50: CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
  100: AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
  150: GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
  200: CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
  250: TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
  300: TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT
  350: CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
  400: TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC
  450: GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT

BASE COUNTS:
    A: 129
    C:  97
    G: 119
    T: 155
TOTAL: 500

Go

<lang go>package main

import ( 

   "fmt"
   "sort"

)

func main() { 

   dna := "" +
       "CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG" +
       "CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG" +
       "AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT" +
       "GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT" +
       "CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG" +
       "TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA" +
       "TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT" +
       "CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG" +
       "TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC" +
       "GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT"

   fmt.Println("SEQUENCE:")
   le := len(dna)
   for i := 0; i < le; i += 50 {
       k := i + 50
       if k > le {
           k = le
       }
       fmt.Printf("%5d: %s\n", i, dna[i:k])
   }
   baseMap := make(map[byte]int) // allows for 'any' base
   for i := 0; i < le; i++ {
       baseMap[dna[i]]++
   }
   var bases []byte
   for k := range baseMap {
       bases = append(bases, k)
   }
   sort.Slice(bases, func(i, j int) bool { // get bases into alphabetic order
       return bases[i] < bases[j]
   })

   fmt.Println("\nBASE COUNT:")
   for _, base := range bases {
       fmt.Printf("    %c: %3d\n", base, baseMap[base])
   }
   fmt.Println("    ------")
   fmt.Println("    Σ:", le)
   fmt.Println("    ======")

}</lang>

Output:
SEQUENCE:
    0: CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
   50: CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
  100: AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
  150: GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
  200: CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
  250: TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
  300: TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT
  350: CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
  400: TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC
  450: GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT

BASE COUNT:
    A: 129
    C:  97
    G: 119
    T: 155
    ------
    Σ: 500
    ======

Pascal

<lang pascal>program DNA_Base_Count; {$IFDEF FPC} 

 {$MODE DELPHI}//String = AnsiString

{$ELSE} 

 {$APPTYPE CONSOLE}

{$ENDIF} const 

   dna =
       'CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG' +
       'CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG' +
       'AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT' +
       'GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT' +
       'CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG' +
       'TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA' +
       'TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT' +
       'CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG' +
       'TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC' +
       'GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT';

var 

 CntIdx : array of NativeUint;
 DNABases : String;
 SumBaseTotal : NativeInt;

procedure OutFormatBase(var DNA: String;colWidth:NativeInt); var 

 j: NativeInt;

Begin 

 j := 0;
 Writeln(' DNA base sequence');
 While j<Length(DNA) do
 Begin
   writeln(j:5,copy(DNA,j+1,colWidth):colWidth+2);
   inc(j,colWidth);
 end;
 writeln;

end;

procedure Cnt(const DNA: String); var 

 i,p :NativeInt;

Begin 

 SetLength(CntIdx,Length(DNABases));
 i := 1;
 while i <= Length(DNA) do
 Begin
   p := Pos(DNA[i],DNABases);
   //found new base so extend list
   if p = 0 then
   Begin
     DNABases := DNABases+DNA[i];
     p := length(DNABases);
     Setlength(CntIdx,p+1);
   end;
   inc(CntIdx[p]);
   inc(i);
 end;

 Writeln('Base     Count');
 SumBaseTotal := 0;
 For i := 1 to Length(DNABases) do
 Begin
   p := CntIdx[i];
   inc(SumBaseTotal,p);
   writeln(DNABases[i]:4,p:10);
 end;
 Writeln('Total base count ',SumBaseTotal);
 writeln;

end;

var 

 TestDNA: String;

Begin 

 DNABases :='ACGT';// predefined
 TestDNA := DNA;
 OutFormatBase(TestDNA,50);
 Cnt(TestDNA);

end.</lang>

Output:
 DNA base sequence
    0  CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
   50  CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
  100  AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
  150  GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
  200  CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
  250  TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
  300  TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT
  350  CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
  400  TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC
  450  GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT

Base     Count
   A       129
   C        97
   G       119
   T       155
Total base count 500

Perl 6

Works with: Rakudo version 2019.07.1

It's the Letter frequency task all over again, just simpler and dressed up in different clothes.

The specs for what "pretty print" means are sadly lacking. Ah well, just makes it easily defensible if I do anything at all.

<lang perl6>my $dna = join , lines q:to/END/; 

   CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
   CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
   AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
   GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
   CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
   TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
   TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT
   CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
   TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC
   GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT
   END


put pretty($dna, 80); put "\nTotal bases: ", +my $bases = $dna.comb.Bag; put $bases.sort(~*.key).join: "\n";

sub pretty ($string, $wrap = 50) { 

   $string.comb($wrap).map( { sprintf "%8d: %s", $++ * $wrap, $_ } ).join: "\n"

}</lang>

Output:
       0: CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCG
      80: AGACGGGGTGGTCGATTCTGAGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGATGGGACGTTTC
     160: GTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTTCGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGT
     240: TCTGAGTTGGTCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATATTTAATTTTTCTATATAGCG
     320: ATCTGTATTTAAGCAATTCATTTAGGTTATCGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
     400: TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGACGACCGGGGACTTGCATGATGGGAGCAGCTT
     480: TGTTAAACTACGAACGTAAT

Total bases: 500
A	129
C	97
G	119
T	155

Python

Procedural

<lang python>from collections import Counter

def basecount(dna): 

   return sorted(Counter(dna).items())

def seq_split(dna, n=50): 

   return [dna[i: i+n] for i in range(0, len(dna), n)]

def seq_pp(dna, n=50): 

   for i, part in enumerate(seq_split(dna, n)):
       print(f"{i*n:>5}: {part}")
   print("\n  BASECOUNT:")
   tot = 0
   for base, count in basecount(dna):
       print(f"    {base:>3}: {count}")
       tot += count
   base, count = 'TOT', tot
   print(f"    {base:>3}= {count}")

if __name__ == '__main__': 

   print("SEQUENCE:")
   sequence = \

CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG\ CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG\ AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT\ GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT\ CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG\ TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA\ TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT\ CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG\ TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC\ GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT 

   seq_pp(sequence)

</lang>

Output:
SEQUENCE:
    0: CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
   50: CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
  100: AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
  150: GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
  200: CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
  250: TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
  300: TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT
  350: CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
  400: TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC
  450: GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT

  BASECOUNT:
      A: 129
      C: 97
      G: 119
      T: 155
    TOT= 500

Functional

Sequence and base counts displayed in GenBank format.

Works with: Python version 3.7

<lang python>Bioinformatics – base count

from itertools import count from functools import reduce


  1. genBankFormatWithBaseCounts :: String -> String

def genBankFormatWithBaseCounts(sequence): 

   DNA Sequence displayed in a subset of the GenBank format.
      See example at foot of:
      https://www.genomatix.de/online_help/help/sequence_formats.html
   
   ks, totals = list(zip(*baseCounts(sequence)))
   ns = list(map(str, totals))
   w = 2 + max(map(len, ns))

   return '\n'.join([
       'DEFINITION  len=' + str(sum(totals)),
       'BASE COUNT  ' + .join([
           n.rjust(w) + ' ' + k.lower() for (k, n)
           in zip(ks, ns)
       ]),
       'ORIGIN'
   ] + [
       str(i).rjust(9) + ' ' + k for i, k
       in zip(
           count(1, 60),
           [
               ' '.join(row) for row in
               chunksOf(6)(chunksOf(10)(sequence))
           ]
       )
   ] + ['//'])


  1. baseCounts :: String -> Zip [(String, Int)]

def baseCounts(baseString): 

   Sums of each base type in the given sequence string.
   bases = {
       'A': 0,
       'C': 1,
       'G': 2,
       'T': 3
   }
   return zip(
       list(bases.keys()) + ['Other'],
       foldl(
           lambda a: compose(
               nthArrow(succ)(a),
               flip(curry(bases.get))(4)
           )
       )((0, 0, 0, 0, 0))(baseString)
   )


  1. --------------------------TEST---------------------------
  2. main :: IO ()

def main(): 

   Base counts and sequence displayed in GenBank format
   
   print(
       genBankFormatWithBaseCounts(\

CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG\ CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG\ AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT\ GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT\ CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG\ TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA\ TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT\ CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG\ TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC\ GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT) 

   )


  1. -------------------------GENERIC-------------------------
  1. chunksOf :: Int -> [a] -> a

def chunksOf(n): 

   A series of lists of length n, subdividing the
      contents of xs. Where the length of xs is not evenly
      divible, the final list will be shorter than n.
   
   return lambda xs: reduce(
       lambda a, i: a + [xs[i:n + i]],
       range(0, len(xs), n), []
   ) if 0 < n else []


  1. compose :: ((a -> a), ...) -> (a -> a)

def compose(*fs): 

   Composition, from right to left,
      of a series of functions.
   
   return lambda x: reduce(
       lambda a, f: f(a),
       fs[::-1], x
   )


  1. curry :: ((a, b) -> c) -> a -> b -> c

def curry(f): 

   A curried function derived
      from an uncurried function.
   
   return lambda x: lambda y: f(x, y)


  1. flip :: (a -> b -> c) -> b -> a -> c

def flip(f): 

   The function f with its
      arguments reversed.
   
   return lambda a: lambda b: f(b)(a)


  1. foldl :: (a -> b -> a) -> a -> [b] -> a

def foldl(f): 

   Left to right reduction of a list,
      using the binary operator f, and
      starting with an initial value a.
   
   def go(acc, xs):
       return reduce(lambda a, x: f(a)(x), xs, acc)
   return lambda acc: lambda xs: go(acc, xs)


  1. nthArrow :: (a -> b) -> Tuple -> Int -> Tuple

def nthArrow(f): 

   A simple function lifted to one which applies
      to a tuple, transforming only its nth value.
   
   def go(v, n):
       return v if n > len(v) else [
           x if n != i else f(x)
           for i, x in enumerate(v)
       ]
   return lambda tpl: lambda n: tuple(go(tpl, n))


  1. succ :: Enum a => a -> a

def succ(x): 

   The successor of a value.
      For numeric types, (1 +).
   
   return 1 + x


  1. MAIN ---

if __name__ == '__main__': 

   main()</lang>
Output:
DEFINITION  len=500
BASE COUNT    129 a   97 c  119 g  155 t    0 other
ORIGIN
        1 CGTAAAAAAT TACAACGTCC TTTGGCTATC TCTTAAACTC CTGCTAAATG CTCGTGCTTT
       61 CCAATTATGT AAGCGTTCCG AGACGGGGTG GTCGATTCTG AGGACAAAGG TCAAGATGGA
      121 GCGCATCGAA CGCAATAAGG ATCATTTGAT GGGACGTTTC GTCGACAAAG TCTTGTTTCG
      181 AGAGTAACGG CTACCGTCTT CGATTCTGCT TATAACACTA TGTTCTTATG AAATGGATGT
      241 TCTGAGTTGG TCAGTCCCAA TGTGCGGGGT TTCTTTTAGT ACGTCGGGAG TGGTATTATA
      301 TTTAATTTTT CTATATAGCG ATCTGTATTT AAGCAATTCA TTTAGGTTAT CGCCGCGATG
      361 CTCGGTTCGG ACCGCCAAGC ATCTGGCTCC ACTGCTAGTG TCCTAAATTT GAATGGCAAA
      421 CACAAATAAG ATTTAGCAAT TCGTGTAGAC GACCGGGGAC TTGCATGATG GGAGCAGCTT
      481 TGTTAAACTA CGAACGTAAT
//

REXX

A little extra boilerplate was added to verify correct coding of the bases in a DNA string and the alignment of the (totals) numbers. <lang rexx>/*REXX program finds the number of each base in a DNA string (along with a total). */ parse arg dna . if dna== | dna=="," then dna= CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG , 

                                CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG ,
                                AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT ,
                                GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT ,
                                CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG ,
                                TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA ,
                                TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT ,
                                CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG ,
                                TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC ,
                                GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT

dna= space(dna, 0); upper dna /*elide blanks from DNA; uppercase it. */ say '────────length of the DNA string: ' length(dna) @.=0 /*initialize the count for all bases. */ w= 1 /*the maximum width of a base count. */ $= /*a placeholder for the names of bases.*/ 

      do j=1  for length(dna)                   /*traipse through the  DNA  string.    */
      _= substr(dna, j, 1)                      /*obtain a base name from the DNA str. */
      if pos(_, $)==0  then $=$ || _            /*if not found before, add it to list. */
      @._= @._ + 1                              /*bump the count of this base.         */
      w= max(w, length(@._) )                   /*compute the maximum width number.    */
      end   /*j*/

say 

      do k=0  for 255;   z= d2c(k)              /*traipse through all possibilities.   */
      if pos(z, $)==0  then iterate             /*Was this base found?  No, then skip. */
      say '     base '   z    " has a basecount of: "   right(@.z, w)
      @.tot= @.tot + @.z                        /*add to a grand total to verify count.*/
      end   /*k*/

say /*stick a fork in it, we're all done. */ say '────────total for all basecounts:' right(@.tot, w+1)</lang>

output   when using the default input:
────────length of the DNA string:  500

     base  A  has a basecount of:  129
     base  C  has a basecount of:   97
     base  G  has a basecount of:  119
     base  T  has a basecount of:  155

────────total for all basecounts:  500

zkl

<lang zkl>bases:=

  1. <<<"

CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT" - " \n";

  1. <<<

[0..*,50].zipWith(fcn(n,bases){ println("%6d: %s".fmt(n,bases.concat())) }, 

  bases.walker().walk.fp(50)).pump(Void);  // .pump forces the iterator

println("\nBase Counts: ", bases.counts().pump(String,Void.Read,"%s: %d ".fmt)); println("Total: ",bases.len());</lang>

Output:
     0: CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
    50: CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
   100: AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
   150: GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
   200: CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
   250: TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
   300: TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT
   350: CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
   400: TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC
   450: GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT

Base Counts: A: 129  C: 97  G: 119  T: 155  
Total: 500
Retrieved from "https://rosettacode.org/wiki/Bioinformatics/base_count?oldid=296247"