Bioinformatics/base count

From Rosetta Code
Task
Bioinformatics/base count
You are encouraged to solve this task according to the task description, using any language you may know.

Given this string representing ordered DNA bases: 

CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT
CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC
GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT
  • "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.



C

Reads genome from a file, determines string length to ensure optimal formatting <lang C>

  1. include<string.h>
  2. include<stdlib.h>
  3. include<stdio.h>

typedef struct genome{ 

   char* strand;
   int length;
   struct genome* next;

}genome;

genome* genomeData; int totalLength = 0, Adenine = 0, Cytosine = 0, Guanine = 0, Thymine = 0;

int numDigits(int num){ 

   int len = 1;

   while(num>10){
       num = num/10;
       len++;
   }

   return len;

}

void buildGenome(char str[100]){ 

   int len = strlen(str),i;
   genome *genomeIterator, *newGenome; 

   totalLength += len;

   for(i=0;i<len;i++){
       switch(str[i]){
           case 'A': Adenine++;
               break;
           case 'T': Thymine++;
               break;
           case 'C': Cytosine++;
               break;
           case 'G': Guanine++;
               break;
       };
   }

   if(genomeData==NULL){
       genomeData = (genome*)malloc(sizeof(genome));

       genomeData->strand = (char*)malloc(len*sizeof(char));
       strcpy(genomeData->strand,str);
       genomeData->length = len;

       genomeData->next = NULL;
   }

   else{
       genomeIterator = genomeData;

       while(genomeIterator->next!=NULL)
           genomeIterator = genomeIterator->next;

       newGenome = (genome*)malloc(sizeof(genome));

       newGenome->strand = (char*)malloc(len*sizeof(char));
       strcpy(newGenome->strand,str);
       newGenome->length = len;

       newGenome->next = NULL;
       genomeIterator->next = newGenome;
   }

}

void printGenome(){ 

   genome* genomeIterator = genomeData;

   int width = numDigits(totalLength), len = 0;

   printf("Sequence:\n");

   while(genomeIterator!=NULL){
       printf("\n%*d%3s%3s",width+1,len,":",genomeIterator->strand);
       len += genomeIterator->length;

       genomeIterator = genomeIterator->next;
   }

   printf("\n\nBase Count\n----------\n\n");

   printf("%3c%3s%*d\n",'A',":",width+1,Adenine);
   printf("%3c%3s%*d\n",'T',":",width+1,Thymine);
   printf("%3c%3s%*d\n",'C',":",width+1,Cytosine);
   printf("%3c%3s%*d\n",'G',":",width+1,Guanine);
   printf("\n%3s%*d\n","Total:",width+1,Adenine + Thymine + Cytosine + Guanine);

   free(genomeData);

}

int main(int argc,char** argv) { 

   char str[100];
   int counter = 0, len;
   
   if(argc!=2){
       printf("Usage : %s <Gene file name>\n",argv[0]);
       return 0;
   }

   FILE *fp = fopen(argv[1],"r");

   while(fscanf(fp,"%s",str)!=EOF)
       buildGenome(str);
   fclose(fp);

   printGenome();

   return 0;

} </lang> Run and output : 

abhishek_ghosh@Azure:~/doodles$ ./a.out genome.txt
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
  T  : 155
  C  :  97
  G  : 119

Total: 500

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 ] keep
   [ * 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
    ======

Julia

<lang julia>const sequence = "CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG" * "CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG" * "AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT" * "GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT" * "CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG" * "TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA" * "TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT" * "CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG" * "TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC" * "GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT"

function dnasequenceprettyprint(seq, colsize=50) 

   println(length(seq), "nt DNA sequence:\n")
   rows = [seq[i:min(length(seq), i + colsize - 1)] for i in 1:colsize:length(seq)]
   for (i, r) in enumerate(rows)
       println(lpad(colsize * (i - 1), 5), "   ", r)
   end

end

dnasequenceprettyprint(sequence)

function printcounts(seq) 

   bases = [['A', 0], ['C', 0], ['G', 0], ['T', 0]]
   for c in seq, base in bases
       if c == base[1]
           base[2] += 1
       end
   end
   println("\nNucleotide counts:\n")
   for base in bases
       println(lpad(base[1], 10), lpad(string(base[2]), 12))
   end
   println(lpad("Other", 10), lpad(string(length(seq) - sum(x[2] for x in bases)), 12))
   println("     _________________\n", lpad("Total", 10), lpad(string(length(seq)), 12))

end

printcounts(sequence)

</lang>

Output:
500nt DNA sequence:

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

Nucleotide counts:

         A         129
         C          97
         G         119
         T         155
     Other           0
     _________________
     Total         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

<lang perl>use strict; use warnings; use feature 'say';

my %cnt; my $total = 0;

while ($_ = ) { 

   chomp;
   printf "%4d: %s\n", $total+1, s/(.{10})/$1 /gr;
   $total += length;
   $cnt{$_}++ for split //

}

say "\nTotal bases: $total"; say "$_: " . ($cnt{$_}//0) for <A C G T>;

__DATA__ CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT</lang>

Output:
   1: CGTAAAAAAT TACAACGTCC TTTGGCTATC TCTTAAACTC CTGCTAAATG
  51: CTCGTGCTTT CCAATTATGT AAGCGTTCCG AGACGGGGTG GTCGATTCTG
 101: AGGACAAAGG TCAAGATGGA GCGCATCGAA CGCAATAAGG ATCATTTGAT
 151: GGGACGTTTC GTCGACAAAG TCTTGTTTCG AGAGTAACGG CTACCGTCTT
 201: CGATTCTGCT TATAACACTA TGTTCTTATG AAATGGATGT TCTGAGTTGG
 251: TCAGTCCCAA TGTGCGGGGT TTCTTTTAGT ACGTCGGGAG TGGTATTATA
 301: TTTAATTTTT CTATATAGCG ATCTGTATTT AAGCAATTCA TTTAGGTTAT
 351: CGCCGCGATG CTCGGTTCGG ACCGCCAAGC ATCTGGCTCC ACTGCTAGTG
 401: TCCTAAATTT GAATGGCAAA CACAAATAAG ATTTAGCAAT TCGTGTAGAC
 451: GACCGGGGAC TTGCATGATG GGAGCAGCTT TGTTAAACTA CGAACGTAAT

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

Phix

<lang Phix>constant dna = substitute(""" CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT ""","\n","") sequence acgt = repeat(0,5) for i=1 to length(dna) do 

   acgt[find(dna[i],"ACGT")] += 1

end for acgt[$] = sum(acgt) sequence s = split(trim(join_by(split(join_by(dna,1,10,""),"\n"),1,5," ")),"\n\n") for i=1 to length(s) do 

   printf(1,"%3d: %s\n",{(i-1)*50+1,s[i]})

end for printf(1,"\nBase counts: A:%d, C:%d, G:%d, T:%d, total:%d\n",acgt)</lang>

Output:
  1: CGTAAAAAAT TACAACGTCC TTTGGCTATC TCTTAAACTC CTGCTAAATG
 51: CTCGTGCTTT CCAATTATGT AAGCGTTCCG AGACGGGGTG GTCGATTCTG
101: AGGACAAAGG TCAAGATGGA GCGCATCGAA CGCAATAAGG ATCATTTGAT
151: GGGACGTTTC GTCGACAAAG TCTTGTTTCG AGAGTAACGG CTACCGTCTT
201: CGATTCTGCT TATAACACTA TGTTCTTATG AAATGGATGT TCTGAGTTGG
251: TCAGTCCCAA TGTGCGGGGT TTCTTTTAGT ACGTCGGGAG TGGTATTATA
301: TTTAATTTTT CTATATAGCG ATCTGTATTT AAGCAATTCA TTTAGGTTAT
351: CGCCGCGATG CTCGGTTCGG ACCGCCAAGC ATCTGGCTCC ACTGCTAGTG
401: TCCTAAATTT GAATGGCAAA CACAAATAAG ATTTAGCAAT TCGTGTAGAC
451: GACCGGGGAC TTGCATGATG GGAGCAGCTT TGTTAAACTA CGAACGTAAT

Base counts: A:129, C:97, G:119, T:155, total:500

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 = 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 for each base type in the given sequence string, with
      a fifth sum for any characters not drawn from {A, C, G, T}.
   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
//

Racket

<lang racket> </lang>

Output:


Raku


(formerly 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


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



Swift


<lang swift>import Foundation

let dna = """



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



print("input:\n\(dna)\n")

let counts =



 dna.replacingOccurrences(of: "\n", with: "").reduce(into: [:], { $0[$1, default: 0] += 1 })



print("Counts: \(counts)")
print("Total: \(counts.values.reduce(0, +))")</lang>





Output:


input:
CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG
CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG
AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT
GGGACGTTTCGTCGACAAAGTCTTGTTTCGAGAGTAACGGCTACCGTCTT
CGATTCTGCTTATAACACTATGTTCTTATGAAATGGATGTTCTGAGTTGG
TCAGTCCCAATGTGCGGGGTTTCTTTTAGTACGTCGGGAGTGGTATTATA
TTTAATTTTTCTATATAGCGATCTGTATTTAAGCAATTCATTTAGGTTAT
CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG
TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC
GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT

["C": 97, "T": 155, "G": 119, "A": 129]
Total: 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=296265"