Bioinformatics/Subsequence: Difference between revisions

=={{header|Nim}}==

<lang Nim>import random, sequtils, strutils

proc dnaSequence(n: Positive): string =

## Create a random DNA sequence of length "n".

newSeqWith(n, sample("ACGT")).join()

proc positions(dnaSeq, subSeq: string): seq[int] =

## Return the list of starting positions of a subsequence

## "subSeq" in a sequence "dnaSeq". Positions start at 1.

var start = 0

while true:

let pos = dnaSeq.find(subSeq, start)

if pos < 0: break

result.add pos + 1

start = pos + 1

when isMainModule:

const

N = 200

Step = 20

randomize()

let dnaSeq = dnaSequence(N)

echo "DNA sequence:"

for i in countup(0, N - 1, Step):

echo ($(i+1)).align(3), ' ', dnaSeq[i..i+(Step-1)]

let subSeq = dnaSequence(3)

echo "\nDNA subsequence: ", subSeq

echo()

let pos = dnaSeq.positions(subSeq)

if pos.len == 0:

echo "Subsequence not found."

else:

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

echo "Subsequence found at position", tail, pos.join(", ")</lang>

{{out}}

<pre>DNA sequence:

1 CACATACGATGAGCTGGGCG

21 CCTAAGAGGCGGAAAGACAA

41 CCGTGTGTGTCTAACCCATG

61 GTTTAATTGCAGATAGTCTC

81 TAGACTACAAACATTAGAGC

101 AATGCACCGGGGTGCACGTG

121 TGTTTTGACTTCCCATGAAA

141 GCCCTTATCCTAGAGTACAG

161 TCGGCAAATGTTCGCTCCTT

181 GGCCCACTCCATTTGGACGG

DNA subsequence: GTT

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