Bioinformatics/Subsequence: Difference between revisions
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→{{header|11l}}: Void
Thundergnat (talk | contribs) m (Automated syntax highlighting fixup (second round - minor fixes)) |
Alextretyak (talk | contribs) m (→{{header|11l}}: Void) |
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R r
F dna_findall(String needle, haystack) ->
V pp = positions(haystack, needle)
I pp.empty
Line 65:
94:98
</pre>
=={{header|Action!}}==
<syntaxhighlight lang="action!">DEFINE SEQLEN="200"
Line 311 ⟶ 312:
600 39 .biosub nl</syntaxhighlight>
{{out}}
<pre> 0: ATTCAAGGAC
10: CACTATTAAC
20: CTGCATTGTG
Line 345:
145..149
289..293
312..316</pre>
</pre>▼
=={{header|FreeBASIC}}==
{{trans|Wren}}
<syntaxhighlight lang="vb">Const base_ = "ACGT"
Sub findDnaSubsequence(dnaSize As Integer, chunkSize As Integer)
Dim As String dnaSeq(1 To dnaSize)
Dim As Integer i, chunk
For i = 1 To dnaSize
dnaSeq(i) = Mid(base_, Int(Rnd * 4)+1, 1)
Next
Dim As String dnaStr
For i = 1 To dnaSize
dnaStr += dnaSeq(i)
Next
Dim As String dnaSubseq(1 To 4)
For i = 1 To 4
dnaSubseq(i) = Mid(base_, Int(Rnd * 4)+1, 1)
Next
Dim As String dnaSubstr
For i = 1 To 4
dnaSubstr += dnaSubseq(i)
Next
Print "DNA sequence:"
For chunk = 1 To Len(dnaStr) Step chunkSize
Print Using "###_._.###: &"; chunk; chunk+chunkSize-1; Mid(dnaStr, chunk, chunkSize)
Next
Print !"\nSubsequence to locate: "; dnaSubstr
Dim As Integer idx = Instr(dnaStr, dnaSubstr)
Print Iif(idx <> 0, "Matches found at the following indices:", "No matches found.")
Do While idx > 0
If idx <> 0 Then Print Using "###_._.###"; idx; idx + 3
idx = Instr(idx+4, dnaStr, dnaSubstr)
Loop
End Sub
findDnaSubsequence(200, 20)
Print
findDnaSubsequence(600, 40)
Sleep</syntaxhighlight>
{{out}}
<pre>DNA sequence:
1.. 20: TTATAGTCTTGGAGGCATGT
21.. 40: TAACTTATGCGGAGCAGACA
41.. 60: CGGAGTATGCATTCCTCTTA
61.. 80: CCAAACGGTGCTGCCCGCGC
81..100: ACTCGCTGTATTCCGTATCG
101..120: TCACATTATCTAAACCACGA
121..140: TTTCCAGCGTGCGTGGGAAG
141..160: GCCATGTTTAGTCGGGGGCC
161..180: AAGGTCTTTGGCTTATGCTG
181..200: TTTTTTTTTCTTCGGTTACA
Subsequence to locate: ATTT
Matches found at the following indices:
120..123
DNA sequence:
1.. 40: GTGCGGGCCGTTAGCAGCTACGAGTGCTAGATGGAACTAG
41.. 80: TCCCCGCTCCCAAATGCAAAGCGTCCCAGACCAGTCTTGA
81..120: AGCCCGTTAAATTACACCTGAACCGTTGCAAATGATCGAT
121..160: AGACGGGGTATAATAGCGGAAAACACAGGGGAACTGCATG
161..200: CAAGCTCGAGCCGCTGAAGGATGGCTCCCCCCCGAGTGTA
201..240: AGTGGATCTCGCCCAAATAGCGGGGGAACAAAGAAAGGTA
241..280: AGTCTTACTTCGCACGTCCCCTCTCATACACGCCAGGACT
281..320: AATGGATCATTCATAGGTGACGGGTGACTTGCGGTGTTTC
321..360: TAGTTGGAGTCACCCGTCAGCTTAGATCTAAGTATGAACC
361..400: GTAAGAGTTTGTAACTGCACCTTCCGTCTCTTCCTCTGTA
401..440: GGAACGCTTTTGCTTGTTATCAGATAGTGTCTCCTTATCA
441..480: TAGGACAGGTTCCTTGTGAAGGTCCACAGAGTTTGCCCGG
481..520: GGTTCGAATATACGACGCTTGTGGTTCCGGCACTATAACT
521..560: TCCGCAGTGTTGTCGACGCCCCTAGCTCCCGGGGTCTTTT
561..600: CGCTTCCCTATAGCGCGAAATGAGTGCAAGGGTACCGGCC
Subsequence to locate: GCAC
Matches found at the following indices:
252..255
377..380
▲510..513</pre>
=={{header|Go}}==
{{trans|Wren}}
Line 785 ⟶ 866:
=={{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.
<syntaxhighlight lang="raku" line>use String::Splice:ver<0.0.3+>;
my $line = 80;
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AGTACTCGACTGTTATGGTAAAAGGGCATCGTGATCGTTTATATTAATCATTGGGACAGGTGGTTAATGTCA<span style="color: #CC0000;">TAGC</span>TTAG<br>
</div>
=={{header|REXX}}==
This REXX version allows the user to specify:
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{{libheader|Wren-str}}
{{libheader|Wren-fmt}}
<syntaxhighlight lang="
import "./pattern" for Pattern
import "./str" for Str
import "./fmt" for Fmt
var rand = Random.new()
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