Bioinformatics/base count: Difference between revisions

 

Given this string representing ordered DNA bases:

CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG

AGGACAAAGGTCAAGATGGAGCGCATCGAACGCAATAAGGATCATTTGAT

CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG

TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC

 

<br><br>

 

=={{header|ALGOL 68}}==

# returns an array of counts of the characters in s that are in c #

# an extra final element holds the count of characters not in c #

FOR i FROM LWB counts TO UPB counts DO counts[ i ] := 0 OD;

FOR i FROM LWB results TO UPB results DO results[ i ] := 0 OD;

FOR i FROM LWB s TO UPB s DO

IF INT ch pos = ABS s[ i ];

# totals #

print( ( newline, "Total: ", whole( total, - width ), newline ) )

{{out}}

<pre>

Total: 500

</pre>

 

=={{header|C}}==

Reads genome from a file, determines string length to ensure optimal formatting

#include<string.h>

#include<stdlib.h>

return 0;

}

Run and output :

<pre>

Total: 500

</pre>

=={{header|C++}}==

Creates a class DnaBase which either uses a provided string or the default DNA sequence.

#include <iostream>

 

 

class DnaBase {

}

}

 

void viewGenome() {

 

std::string genome;

std::map<char, int> count;

};

 

int main(void) {

 

0 :CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG

T : 155

 

 

=={{header|Factor}}==

math.statistics prettyprint qw sequences sorting ;

 

[ "TOTAL: " write [ second ] [ + ] map-reduce . ] bi ;

 

{{out}}

<pre>

TOTAL: 500

</pre>

 

=={{header|Go}}==

 

import (

fmt.Println(" Σ:", le)

fmt.Println(" ======")

 

{{out}}

</pre>

=={{header|Haskell}}==

import Data.List.Split (chunksOf)

import Text.Printf (printf, IsChar(..), PrintfArg(..), fmtChar, fmtPrecision, formatString)

putStrLn "\nBase Counts:"

mapM_ (uncurry (printf "%2s: %2d\n")) $ baseCounts test

{{out}}

<pre>Sequence:

--------

Σ: 500</pre>

=={{header|Java}}==

 

public class orderedSequence {

}

 

public class Sequence {

 

}

 

<pre>

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

 

=={{header|Julia}}==

"CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG" *

"CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG" *

 

printcounts(sequence)

<pre>

500nt DNA sequence:

Total 500

</pre>

 

=={{header|Pascal}}==

{$IFDEF FPC}

{$MODE DELPHI}//String = AnsiString

OutFormatBase(TestDNA,50);

Cnt(TestDNA);

{{out}}

<pre> DNA base sequence

T 155

Total base count 500</pre>

=={{header|Perl}}==

use warnings;

use feature 'say';

CGCCGCGATGCTCGGTTCGGACCGCCAAGCATCTGGCTCCACTGCTAGTG

TCCTAAATTTGAATGGCAAACACAAATAAGATTTAGCAATTCGTGTAGAC

{{out}}

<pre> 1: CGTAAAAAAT TACAACGTCC TTTGGCTATC TCTTAAACTC CTGCTAAATG

G: 119

T: 155</pre>

=={{header|Phix}}==

{{out}}

<pre>

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

</pre>

 

=={{header|Python}}==

===Procedural===

 

def basecount(dna):

GACCGGGGACTTGCATGATGGGAGCAGCTTTGTTAAACTACGAACGTAAT'''

seq_pp(sequence)

 

{{out}}

T: 155

TOT= 500</pre>

 

===Functional===

Sequence and base counts displayed in GenBank format.

{{Works with|Python|3.7}}

 

from itertools import count

# MAIN ---

if __name__ == '__main__':

{{Out}}

<pre>DEFINITION len=500

481 TGTTAAACTA CGAACGTAAT

//</pre>

 

=={{header|Racket}}==

 

 

(define (fold-sequence seq kons #:finalise (finalise (λ x (apply values x))) . k0s)

EOS

)

 

{{out}}

 

TOTAL: 500</pre>

=={{header|Raku}}==

(formerly Perl 6)

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

 

CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG

CTCGTGCTTTCCAATTATGTAAGCGTTCCGAGACGGGGTGGTCGATTCTG

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

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

{{out}}

<pre> 0: CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATGCTCGTGCTTTCCAATTATGTAAGCGTTCCG

G 119

T 155</pre>

=={{header|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.

{{out|output|text=&nbsp; when using the default input:}}

<pre>

 

=={{header|Ring}}==

dna = "" +

"CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG" +

? "C : " + dnaBase["C"]

? "G : " + dnaBase["G"]

{{out}}

<pre>

G : 119

</pre>

 

=={{header|Swift}}==

 

 

let dna = """

 

print("Counts: \(counts)")

 

{{out}}

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

Total: 500</pre>

 

=={{header|Wren}}==

{{libheader|Wren-fmt}}

{{libheader|Wren-sort}}

 

var dna = "CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG" +

System.print(" ------")

System.print(" Σ: %(le)")

 

{{out}}

</pre>

 

 

 

=={{header|zkl}}==

#<<<"

CGTAAAAAATTACAACGTCCTTTGGCTATCTCTTAAACTCCTGCTAAATG

 

println("\nBase Counts: ", bases.counts().pump(String,Void.Read,"%s: %d ".fmt));

{{out}}

<pre>