Bioinformatics/Sequence mutation: Difference between revisions

{{trans|Python}}

 

F nonrandom(n)

:seed = 1664525 * :seed + 1013904223

print(‘ #10 @#.’.format(kind, index))

print()

 

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=={{header|Ada}}==

with Ada.Numerics.Discrete_Random;

with Ada.Text_Io;

Pretty_Print (Sequence);

 

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<pre>Initial sequence:

=={{header|Arturo}}==

 

dna: map 1..200 => [sample bases]

 

print "------------------------------"

prettyPrint dna

 

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=={{header|C}}==

Adenine ( A ) is always swapped for Thymine ( T ) and vice versa. Similarly with Cytosine ( C ) and Guanine ( G ).

#include<stdlib.h>

#include<stdio.h>

return 0;

}

Sample run :

<pre>

 

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

#include <iomanip>

#include <iostream>

sequence_generator::print_sequence(std::cout, sequence);

return 0;

 

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:: :genome <i><Genome Sequence></i>)

<b>All keys are optional. <i><Genome length></i> is discarded when :genome is set.</b>

(defun random_base ()

(random 4))

(t (delete_base genome)))))

(output_genome_info genome "MUTATED"))

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<pre>

 

=={{header|Factor}}==

macros math math.statistics namespaces prettyprint quotations

random sequences sorting ;

[ mutate ] curry times nl "MUTATED " write show-dna ;

 

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<pre>

 

=={{header|Go}}==

 

import (

fmt.Println()

prettyPrint(dna, 50)

 

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</pre>

=={{header|Haskell}}==

import Data.List.Split (chunksOf)

import System.Random (Random, randomR, random, newStdGen, randoms, getStdRandom)

showSequence = mapM_ (uncurry (printf "%3d: %s\n")) . chunkedDNASequence

showBaseCounts = mapM_ (uncurry (printf "%s: %3d\n")) . baseCounts

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<pre>Initial Sequence:

 

=={{header|J}}==

MUTS=: ;: 'del ins mut'

 

)

 

 

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=={{header|Java}}==

import java.util.Random;

 

private static final int OP_COUNT = 3;

private static final char[] BASES = {'A', 'C', 'G', 'T'};

 

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=={{header|JavaScript}}==

const numBases = 250

const numMutations = 30

console.log('\nMUTATED BASE COUNTS:')

printBases(mut);

 

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=={{header|Julia}}==

randpos(seq) = rand(1:length(seq)) # 1

mutateat(pos, seq) = (s = seq[:]; s[pos] = rand(dnabases); s) # 2-1

 

testbioseq()

<pre>

500nt DNA sequence:

=={{header|Lua}}==

Using the <code>prettyprint()</code> function from [[Bioinformatics/base_count#Lua]] (not replicated here)

bases = {"A","C","T","G"}

function randbase() return bases[math.random(#bases)] end

 

print("MUTATED:")

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<pre>ORIGINAL:

=={{header|Mathematica}} / {{header|Wolfram Language}}==

BioSequence is a fundamental data type in Mathematica:

seq = BioSequence["DNA", "ATAAACGTACGTTTTTAGGCT"];

randompos = RandomInteger[seq["SequenceLength"]];

ends = Rest[Accumulate[Prepend[StringLength /@ parts, 0]]];

StringRiffle[MapThread[ToString[#1] <> "-" <> ToString[#2] <> ": " <> #3 &, {begins, ends, parts}], "\n"]

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<pre>1-50: TAGCAGGGGAATTGTCGACTCCCGGGTTTCAATTGCCAACCAAGCATATT

 

=={{header|Nim}}==

import strformat

import strutils

echo "\nMutated sequence"

echo "————————————————\n"

 

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=={{header|Perl}}==

{{trans|Raku}}

use warnings;

use feature 'say';

say "Total bases: ". length $mutate;

say "$_: $cnt{$_}" for @bases;

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<pre>Original DNA strand:

 

=={{header|Phix}}==

<span style="color: #004080;">string</span> <span style="color: #000000;">dna</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">repeat</span><span style="color: #0000FF;">(</span><span style="color: #008000;">' '</span><span style="color: #0000FF;">,</span><span style="color: #000000;">200</span><span style="color: #0000FF;">+</span><span style="color: #7060A8;">rand</span><span style="color: #0000FF;">(</span><span style="color: #000000;">300</span><span style="color: #0000FF;">))</span>

<span style="color: #008080;">for</span> <span style="color: #000000;">i</span><span style="color: #0000FF;">=</span><span style="color: #000000;">1</span> <span style="color: #008080;">to</span> <span style="color: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">dna</span><span style="color: #0000FF;">)</span> <span style="color: #008080;">do</span> <span style="color: #000000;">dna</span><span style="color: #0000FF;">[</span><span style="color: #000000;">i</span><span style="color: #0000FF;">]</span> <span style="color: #0000FF;">=</span> <span style="color: #008000;">"ACGT"</span><span style="color: #0000FF;">[</span><span style="color: #7060A8;">rand</span><span style="color: #0000FF;">(</span><span style="color: #000000;">4</span><span style="color: #0000FF;">)]</span> <span style="color: #008080;">end</span> <span style="color: #008080;">for</span>

<span style="color: #000000;">mutate</span><span style="color: #0000FF;">()</span>

<span style="color: #000000;">show</span><span style="color: #0000FF;">()</span>

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<pre>

 

=={{header|PureBasic}}==

#SEQLEN=200

#PROTOCOL=#True

PrintN("After 10 mutations:")

pprint()

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<pre>Initial sequence:

Similarly parameter choice is chosen from to give the base for substitution or insertion - the more any base appears, the more likely it is to be chosen in any insertion/substitution.

from collections import Counter

 

print(f" {kind:>10} @{index}")

print()

 

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<code>prettyprint</code> and <code>tallybases</code> are defined at [[Bioinformatics/base count#Quackery]].

 

 

[ $ "" swap times

cr cr say "Mutating..." cr

10 times mutate

 

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=={{header|Racket}}==

 

 

(define current-S-weight (make-parameter 1))

(define s+d (parameterize ((current-D-weight 5)) (for/fold ((s initial-sequence)) ((_ 10)) (mutate s))))

(newline)

 

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# The DNA strand

sub diff ($orig, $repl) {

($orig.comb Z $repl.comb).map( -> ($o, $r) { $o eq $r ?? $o !! $r.lc }).join

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<pre>ORIGINAL DNA STRAND:

 

=={{header|Ring}}==

row = 0

dnaList = []

total = dnaBase["A"] + dnaBase["T"] + dnaBase["C"] + dnaBase["G"]

see "Total: " + total+ nl + nl

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<pre>

 

=={{header|Ruby}}==

attr_accessor :seq

test.delete

puts test

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<pre> 0 TAAGGTGAGGAGTGTGATGGAGTTCGGTGGCTAGCCACAAATACAACACA

=={{header|Swift}}==

 

 

enum Action: CaseIterable {

}

 

 

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=={{header|Vlang}}==

{{trans|Go}}

import rand.seed

 

println('')

pretty_print(dna, 50)

 

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{{libheader|Wren-sort}}

{{libheader|Wren-fmt}}

import "/fmt" for Fmt

import "/sort" for Sort

for (i in 0...muts) dna = mutate.call(dna, w)

System.print()

 

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=={{header|Yabasic}}==

{{trans|Phix}}

// by Galileo, 07/2022

 

show()

mutate()

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<pre>1: TCCATCGTGG GATCGCTCTA GCGGTATGCT ATCATTCCTA TAGCAATTCT

 

=={{header|zkl}}==

dna:=(190).pump(Data().howza(3),(0).random.fp(0,4),bases.get); // bucket of bytes

 

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

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

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<pre>

 

=={{header|Rust}}==

use rand::prelude::*;

use std::collections::HashMap;

println!("\nMutated sequence:\n{}", seq);

}

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<pre>