Bioinformatics/Subsequence: Difference between revisions

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<lang ecmascript>import "random" for Random

import "/pattern" for Pattern

import "/str" for Str

import "/fmt" for Fmt

var rand = Random.new()

var base = "ACGT"

var findDnaSubsequence = Fn.new { |dnaSize, chunkSize|

var dnaSeq = List.filled(dnaSize, null)

for (i in 0...dnaSize) dnaSeq[i] = base[rand.int(4)]

var dnaStr = dnaSeq.join()

var dnaSubseq = List.filled(4, null)

for (i in 0...4) dnaSubseq[i] = base[rand.int(4)]

var dnaSubstr = dnaSubseq.join()

System.print("DNA sequence:")

var i = chunkSize

for (chunk in Str.chunks(dnaStr, chunkSize)) {

Fmt.print("$3d..$3d: $s", i - chunkSize + 1, i, chunk)

i = i + chunkSize

}

System.print("\nSubsequence to locate: %(dnaSubstr)")

var p = Pattern.new(dnaSubstr)

var matches = p.findAll(dnaStr)

if (matches.count == 0) {

System.print("No matches found.")

} else {

System.print("Matches found at the following indices:")

for (m in matches) {

Fmt.print("$3d..$3d", m.index + 1, m.index + 4)

}

}

}

findDnaSubsequence.call(200, 20)

System.print()

findDnaSubsequence.call(600, 40)</lang>

{{out}}

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DNA sequence:

1.. 20: TATGGGCGCATTATGACAAC

21.. 40: GGCTACTGAAACGAAAATTC

41.. 60: ATGCCTTCGGAGGCTAGACC

61.. 80: ACTCATACATGATTTACAGC

81..100: TAGTCAGTTGCGTCCGCCAT

101..120: CCCGCATAACTATGTATTAC

121..140: GAGCATGTTCTGGCAACCTT

141..160: TCAGTGACAGTTCCTCAGGC

161..180: GCGTTCGCGTTGAAGGCCTC

181..200: CCCACACCGCACCCCTGCCG

Subsequence to locate: AATT

Matches found at the following indices:

36.. 39

DNA sequence:

1.. 40: GCGCTGAGCGCCCCAGTACAGCGGGTTAAACCGAGCCCGC

41.. 80: TCCGATGAACCAACTCCCATTCCTATAATGGTGCCCCGAC

81..120: ATATTGAATTCGGCGGGTCCGCTATCGGGCTGAGGATGCC

121..160: AATATCTAGGCGCTACCCTGAAGATCCTCAGTTGTGGTGT

161..200: CGCGGAGTGTCGATCCCAGAGCTCCCAATTGACTCAATTA

201..240: CTTTTTCCGTCCTCTTGCTTACGGATTTATGTTTGTGGCA

241..280: GAGGTTATGCTTCAGGCATCCCCATGTTTCCTGAGATACG

281..320: ACCACTGTCAGGTGGCTTGAATCTACCTTGTATTTCCTCT

321..360: AGTACCAGTCACTGTCATCTACTGGAAGCCATATCAGCGT

361..400: TGAAATGTCTATAATTTACTCTCCGGTTGTACCCAAGCGA

401..440: TAACAGCAACGTGTGGGTCTAAAGAGTTCCGCGTTTCGAC

441..480: ATAACGTGCTCCTATTTATCTACCGAAACACCCTATTTTC

481..520: CATCTAACCGGCACCCAATGCGCAGGTGTACGCGTCCTAC

521..560: TACGTTTGAAACGGTTCCATCTCGCCATGTACAATTGTGG

561..600: GGCTACGATTAAGTGTAGTCGGTAATTCAGGGTGAAGTTG

Subsequence to locate: TTCG

Matches found at the following indices:

89.. 92

435..438