Bioinformatics/Subsequence

Bioinformatics/Subsequence is a draft programming task. It is not yet considered ready to be promoted as a complete task, for reasons that should be found in its talk page.

Task

Genarate randomly a string (200 elements) of characters A, C, G, and T representing a DNA sequence write a routine to find the position of subsequence (also generating randomly).
Let length of subsequence equal to 4

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. <lang perl6>use String::Splice:ver<0.0.3>;

my $line = 80;

my $haystack = [~] <A C G T>.roll($line * 8);

say 'Needle: ' ~ my $needle = [~] <A C G T>.roll(4);

my $these = $haystack ~~ m:g/<$needle>/;

my @match = $these.map: { .from, .pos }

printf "From: %3s to %3s\n", |$_ for @match;

my $disp = $haystack.comb.batch($line)».join.join("\n");

for @match.reverse {

   $disp.=&splice(.[1] + .[1] div $line, "\e[0m" );
   $disp.=&splice(.[0] + .[0] div $line, "\e[31m");

}

say $disp;</lang>

Output:

Show in custom div to better display highlighting.

Needle: TAGC
From: 159 to 163
From: 262 to 266
From: 315 to 319
From: 505 to 509
From: 632 to 636
CATATGTGACACTGACAGCTCGCGCGAAAATCCGTGTGACGGTCTGAACACTATACTATAGGCCCGGTCGGCATTTGTGG
CTCCCCAGTGGAGAGACCACTCGTCAATTGCTGACGACTTAACACAAATCGAGTCGCCCTTAGTGCCAGACGGGACTCCT
AGCAAAGGGCGGCACGTGGTGACTCCCAATATGTGAGCATGCCATCTAATTGATCTGGGGGGTTTCGCGGGAATACCTAG
GGGCGTTCTGTCCATGGATCTCTAGCCCTGCGAAGAGATACCCGCAGTGAGTTGCACGTGCAAAGAACTTGTAACTAGCG
TATTCTGTATCCGCCGCGCGATATGCTTCTGCGGGATGTACTTCTTGTGACTAAGACTTTGTTATCCAAATTGACCAATA
TTCAACGGTCGACTCTCCGAGGCAGTATCGGTACGCCGAAAAATGGTTACTTCGGCCATACGTAACCTCTCAAGTCACGA
TTACAGCCCACGGGGGCTTACAGCATAGCTCCAAAGACATTCCAATTGAGCTACAACGTGTTCAGTGCGGAGCAGTATCC
AGTACTCGACTGTTATGGTAAAAGGGCATCGTGATCGTTTATATTAATCATTGGGACAGGTGGTTAATGTCATAGCTTAG

REXX

<lang rexx></lang> output

Ring

<lang ring> row = 0 dnaList = [] base = ["A","C","G","T"] long = 20 see "DNA sequence:" + nl see " " + long + ": "

for nr = 1 to 200

   row = row + 1
   rnd = random(3)+1
   baseStr = base[rnd]
   see baseStr # + " "
   if (row%20) = 0 and long < 200
       long = long + 20
       see nl
       if long < 100
          see " " + long + ": "
       else
          see "" + long + ": "
       ok
   ok
   add(dnaList,baseStr)

next

strBase = "" for n = 1 to 4

   rnd = random(3)+1
   strBase = strBase + base[rnd]

next

see "subsequence to search: " + strBase + nl

seqok = 0

for n = 1 to 196

   flag = 1
   for m = 0 to 3
       if dnaList[n+m] != strBase[m+1]
          flag = 0
          exit
       ok
   next
   if flag = 1
      seqok = 1
      see "start position of sequence = " + n + nl
   ok

next

if seqok = 0

  see "subsequence not found" + nl

ok </lang>

Output:

DNA sequence:
 20: GAGTATAAAAAGCGACATAG
 40: AAGCAGGGGGGGAACAGACA
 60: ACAATTGTGAAAACTAATCA
 80: ATACGGAAAAGGATAAACAT
100: GAGGGACTGCGGTTGGTAGG
120: CGATGAAACCTAAGAATGAA
140: AACGAGGAAGGTGTAAAGTG
160: ATGGGGTCATGGGACAGACA
180: TAGCTAAATGGATAAAAGCG
200: GGTGAAGTCGGTCGCAAACG
subsequence to search: ATGA
start position of subsequence = 79
start position of subsequence = 103
start position of subsequence = 116

Wren

Library: Wren-pattern

Library: Wren-str

Library: Wren-fmt

<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>

Output:

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