Bioinformatics/Subsequence: Difference between revisions

Write a routine to find all the positions of a randomly generated subsequence   (four letters).

<br><br>

=={{header|11l}}==

{{trans|Python}}

 

F nonrandom_choice(lst)

:seed = (1664525 * :seed + 1013904223) [&] FFFF'FFFF

R r

 

V pp = positions(haystack, needle)

I pp.empty

print("\nSearch Sample: "sample_seq)

 

 

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=={{header|Action!}}==

DEFINE SUBLEN="4"

 

PrintE("Not found")

FI

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[https://gitlab.com/amarok8bit/action-rosetta-code/-/raw/master/images/Bioinformatics_subsequence.png Screenshot from Atari 8-bit computer]

83-86

</pre>

=={{header|Ada}}==

with Ada.Strings.Fixed;

with Ada.Numerics.Discrete_Random;

New_Line;

end loop;

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<pre>Search sequence:

Found at position: 371..374

Found at position: 380..383</pre>

=={{header|Arturo}}==

 

randSeq: join map 1..200 => [sample bases]

randSub: join map 1..4 => [sample bases]

print ["Found subsequence at position:" idx]

idx: idx + 1

 

{{out}}

Found subsequence at position: 71

Found subsequence at position: 169</pre>

=={{header|Factor}}==

{{works with|Factor|0.99 2021-02-05}}

math.functions.integer-logs math.parser random regexp sequences ;

 

 

80 10 .biosub nl

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10: CACTATTAAC

20: CTGCATTGTG

145..149

289..293

 

=={{header|Go}}==

{{trans|Wren}}

 

import (

fmt.Println()

findDnaSubsequence(600, 40)

 

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388..391

</pre>

=={{header|jq}}==

{{works with|jq}}

`jot -r N MIN MAX` but a fourth argument can also be

used to specify a seed. An alternative would be to use `gshuf` along the lines of:

# For 200 pseudo-random integers in the range 0 to 3 inclusive:

gshuf -i 0-3 -r -n 200 --random-source=/dev/random

 

Note that the indices shown below are offsets (i.e., the index origin is taken to be 0).

#!/bin/bash

 

"Zero-based indices of \($four):",

($strand | indices($four) | join(" "))

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<pre>

55 141 169

</pre>

=={{header|Julia}}==

 

DNAsearch(needle, haystack, lap=true) = findall(needle, haystack, overlap=lap)

println("Search sequence:\n$rand_string\nfor substring $subseq. Found at positions: ")

foreach(p -> print(rpad(p[2], 8), p[1] % 10 == 0 ? "\n" : ""), enumerate(DNAsearch(subseq, rand_string)))

<pre>

Search sequence:

21:24 74:77 99:102

</pre>

=={{header|Nim}}==

 

proc dnaSequence(n: Positive): string =

else:

let tail = if pos.len == 1: ": " else: "s: "

 

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Subsequence found at positions: 61, 122, 170</pre>

=={{header|Perl}}==

use warnings;

use feature 'say';

say "Target: $target";

say 'Matches at these positions:';

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<pre>Target: CCTG

TGCGAG >CCTG< TAGAGCCGGGCCTCAAATTAAACGAAAAAT

ATAAGTTTGCTTGGCACGCTGTACTACTTATCC >CCTG< ACT</pre>

=={{header|Phix}}==

Currently only searches for non-overlapped sequences, but it should be pretty obvious how to change that, in which case the next underline will simply partially overwrite the previous, so you'll get eg "<=<==>".

<span style="color: #008080;">with</span> <span style="color: #008080;">javascript_semantics</span>

<span style="color: #004080;">sequence</span> <span style="color: #000000;">idx</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">match_all</span><span style="color: #0000FF;">(</span><span style="color: #000000;">test</span><span style="color: #0000FF;">,</span><span style="color: #000000;">dna</span><span style="color: #0000FF;">)</span>

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

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with cheat enabled

GCTA does not occur

</pre>

=={{header|Python}}==

 

{{libheader|regex}}

 

from random import choice

import regex as re

 

dna_findall(sample_seq, dna_seq)

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167:171

</pre>

=={{header|Racket}}==

 

 

(define (rand-seq n)

sub (report-sequence full) (subsequence-indices full sub)))

 

 

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350 : GGCCTCGACCCAATTTAACCTCCCACTCCGTGGGTACAGCTTGAACCCCC

((245 . 248) (250 . 253) (329 . 332) (386 . 389))</pre>

=={{header|Raku}}==

Chances are actually pretty small that a random 4 codon string will show up at all in a random 200 codon sequence. Bump up the sequence size to get a reasonable chance of multiple matches.

 

my $line = 80;

}

 

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Show in custom div to better display highlighting.

:* &nbsp; DNA proteins to be searched in the data &nbsp; &nbsp; &nbsp; &nbsp; (the default is four unique random proteins).

:* &nbsp; the seed for the RANDOM function so runs can be repeated with the same data &nbsp; &nbsp; (no default).

parse arg totLen rndLen basePr oWidth Bevery rndDNA seed .

if totLen=='' | totLen=="," then totLen= 200 /*Not specified? Then use the default.*/

if $\=='' then say right(idx, 7)"│" strip($, 'T') /*show residual protein data*/

say "───────┴"center('' , oWidth+10, '─')

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

<pre>

the random DNA proteins were found in positions: 5 6 16 69 157 158 159 340 796 797 962 963

</pre>

=={{header|Ring}}==

/*-----------------------------------

# Project : DNA subsequences

 

//-----------------------------------------

 

'''Output:'''

 

[https://i.imgur.com/5hhbRBK.mp4 Bioinformatics/Subsequence - video]

=={{header|Wren}}==

{{libheader|Wren-pattern}}

{{libheader|Wren-str}}

{{libheader|Wren-fmt}}

 

var rand = Random.new()

findDnaSubsequence.call(200, 20)

System.print()

 

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