Bioinformatics/Subsequence: Difference between revisions
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Write a routine to find all the positions of a randomly generated subsequence (four letters).
<br><br>
=={{header|11l}}==
{{trans|Python}}
<syntaxhighlight lang="11l">UInt32 seed = 34
F nonrandom_choice(lst)
:seed = (1664525 * :seed + 1013904223) [&] FFFF'FFFF
R lst[Int(:seed >> 16) % lst.len]
F generate_sequence(Int n)
R ((0 .< n).map(_ -> nonrandom_choice([‘A’, ‘C’, ‘G’, ‘T’]))).join(‘’)
F positions(dnaSeq, subSeq)
[Int] r
V start = 0
L
V? pos = dnaSeq.find(subSeq, start)
I pos == N
L.break
r.append(pos)
start = pos + 1
R r
F dna_findall(String needle, haystack) -> N
V pp = positions(haystack, needle)
I pp.empty
print(‘No matches found’)
E
print(‘Found ’needle‘ at the following indices:’)
L(p) pp
print(p‘:’(p + needle.len))
V dna_seq = generate_sequence(200)
V sample_seq = generate_sequence(4)
V c = 1
L(i) dna_seq
I c % 20 != 0 {print(i, end' ‘’)} E print(i)
c++
print("\nSearch Sample: "sample_seq)
dna_findall(sample_seq, dna_seq)</syntaxhighlight>
{{out}}
<pre>
GAAGTGCTCAAACCCTTTTT
CCTTGCCGTAGGTTGTGCTG
CCGCCGCACACCCGCAACAG
CTTTTAGGCATAAGTATACG
GACCGCGGACGGGGCGTAAC
GGTGAACATTTTGCTAAATT
GGCTCTAGGGATGAGCCCTA
TAGCGCTGGGGACTACGCCC
CGGTAAAGATCGAGGCGACT
CACCGATTGCGCTAGGGACA
Search Sample: CGTA
Found CGTA at the following indices:
26:30
94:98
</pre>
=={{header|Action!}}==
<syntaxhighlight lang="action!">DEFINE SEQLEN="200"
DEFINE SUBLEN="4"
PROC RandomSeq(CHAR ARRAY s BYTE len)
CHAR ARRAY letters="ACGT"
BYTE i
FOR i=1 TO len
DO
s(i)=letters(Rand(4)+1)
OD
s(0)=len
RETURN
PROC PrintSeq(CHAR ARRAY s)
BYTE i
FOR i=1 TO s(0)
DO
IF i MOD 20=1 THEN
IF i<10 THEN Put(32) FI
IF i<100 THEN Put(32) FI
PrintB(i)
Print(": ")
FI
Put(s(i))
IF i MOD 20=0 THEN
PutE()
FI
OD
RETURN
BYTE FUNC StartsWith(CHAR ARRAY s,prefix BYTE start)
BYTE i
FOR i=1 TO prefix(0)
DO
IF s(start+i-1)#prefix(i) THEN
RETURN (0)
FI
OD
RETURN (1)
PROC Main()
CHAR ARRAY seq(SEQLEN+1),sub(SUBLEN+1)
BYTE i,notfirst
RandomSeq(seq,SEQLEN)
RandomSeq(sub,SUBLEN)
PrintE("Search sequence:")
PrintSeq(seq)
PutE()
PrintF("Subsequence to find: %S%E%E",sub)
PrintE("Found subsequence at positions:")
notfirst=0
FOR i=1 TO SEQLEN-SUBLEN
DO
IF StartsWith(seq,sub,i) THEN
IF notfirst THEN
Print(", ")
FI
notfirst=1
PrintF("%I-%I",i,i+SUBLEN-1)
FI
OD
IF notfirst=0 THEN
PrintE("Not found")
FI
RETURN</syntaxhighlight>
{{out}}
[https://gitlab.com/amarok8bit/action-rosetta-code/-/raw/master/images/Bioinformatics_subsequence.png Screenshot from Atari 8-bit computer]
<pre>
Search sequence:
1: CGACTCAGGAAGGCCACGTG
21: GTAACTTCTTAGTTACCGTA
41: AGGCTAATAGCTAGCGCTGC
61: GTGACCAGGCATAGTAACCG
81: GCACGCACGTTCACCAAGGG
101: GTCCCGATGGGAGGCACGTT
121: ACTACTCCAAGAACTGTAGT
141: AAGTTACCGAAAAGTTCTCA
161: TCCTTGGGTAGTGAGTACTT
181: TGTGCTATGAAAAATAAGGA
Subsequence to find: ACGC
Found subsequence at positions:
83-86
</pre>
=={{header|Ada}}==
<syntaxhighlight lang="ada">with Ada.Text_Io;
with Ada.Strings.Fixed;
with Ada.Numerics.Discrete_Random;
procedure Sub_Sequence is
type Nucleotide is (A, C, G, T);
function To_Character (N : Nucleotide) return Character
is (case N is
when A => 'A', when C => 'C',
when G => 'G', when T => 'T');
package Random_Nucleotide is new Ada.Numerics.Discrete_Random (Nucleotide);
use Random_Nucleotide;
package Position_Io is new Ada.Text_Io.Integer_Io (Natural);
use Ada.Text_Io;
procedure Put_Bases (Seq : String; Width : Positive) is
First : Natural := Seq'First;
begin
while First < Seq'Last loop
declare
Last : constant Natural :=
Natural'Min (First + Width - 1, Seq'Last);
begin
Position_Io.Put (First); Put ("..");
Position_Io.Put (Last); Put (" ");
Put (Seq (First .. Last));
New_Line;
First := Last + 1;
end;
end loop;
end Put_Bases;
Gen : Generator;
Sequence : String (1 .. 405);
Substring : String (1 .. 4);
Pos : Natural := 0;
begin
Position_Io.Default_Width := 3;
Reset (Gen);
Sequence := (others => To_Character (Random (Gen)));
Substring := (others => To_Character (Random (Gen)));
Put_Line ("Search sequence:");
Put_Bases (Sequence, Width => 50);
New_Line;
Put ("Substring to search: ");
Put (Substring);
New_Line;
loop
Pos := Ada.Strings.Fixed.Index (Sequence, Substring, Pos + 1);
exit when Pos = 0;
Put ("Found at position: ");
Position_Io.Put (Pos); Put ("..");
Position_Io.Put (Pos + Substring'Length - 1);
New_Line;
end loop;
end Sub_Sequence;</syntaxhighlight>
{{out}}
<pre>Search sequence:
1.. 50 CCTACGGAAAAGTGATAAGGACAGATACATAATCCTAAAACCCTGGAAAA
51..100 CTTGTCTCGCCAGAGTAGGGCTCGGCAGGGGGGGCAGTGTTTTAAAACGT
101..150 CAGAGAATAGGCTCTACCTTGTTAGACTGCGAGTACTGGAGCGTAGTTCC
151..200 TATATTGCAAGCTGCTACAGTAAGTATCAAAGTATGCCACACATCCTTCT
201..250 ACAACCGGATTGGTTGCCCAGTAGAAGGCTCGTAGTCACCGGACACGCTG
251..300 TTCTTAAGGTCGGTAAGCTATTACGTCCATGGGAGATTCTCAAGGGTGCG
301..350 TTAGCGGACCCCCGTTACGTCCACGTATCTTCCGTCCAACTACCCCCTAA
351..400 TGTCATTGACATCGCCCGAGTATTTAATTTATTTGAACGGCACCAATTTA
401..405 GAGCT
Substring to search: TATT
Found at position: 153..156
Found at position: 269..272
Found at position: 371..374
Found at position: 380..383</pre>
=={{header|Arturo}}==
<syntaxhighlight lang="rebol">bases: [`A` `G` `C` `T`]
randSeq: join map 1..200 => [sample bases]
randSub: join map 1..4 => [sample bases]
idx: 0
print "Random sequence:"
print join.with:"\n" split.every: 20 randSeq
print ""
print "Looking for subsequence:"
print randSub
print ""
while [(size randSeq) > idx + 4][
if prefix? slice randSeq idx idx+4 randSub ->
print ["Found subsequence at position:" idx]
idx: idx + 1
]</syntaxhighlight>
{{out}}
<pre>Random sequence:
CACGCGCGTTAACCCTGCAT
CTTTTCTCTAAGATGATGCG
CTACTCTGCCCGATTACTAT
GATGTCACCGGCGGTTCGGC
GACTGGCGCTGGCAGAAAGC
GCATGTCAAATTGCCCCAGT
GTGCAAGTCCAAGTATTAGT
GAGGTGCTCCGCTTCGTCCG
GGGTCGACTCGGTCCCACTT
CATTACATGTTGGTAATAGT
Looking for subsequence:
CGGT
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 ;
Line 34 ⟶ 309:
80 10 .biosub nl
600 39 .biosub nl</
{{out}}
<pre> 0: ATTCAAGGAC
10: CACTATTAAC
20: CTGCATTGTG
Line 70 ⟶ 344:
145..149
289..293
312..316</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}}
<syntaxhighlight lang="go">package main
import (
"fmt"
"math/rand"
"regexp"
"time"
)
const base = "ACGT"
func findDnaSubsequence(dnaSize, chunkSize int) {
dnaSeq := make([]byte, dnaSize)
for i := 0; i < dnaSize; i++ {
dnaSeq[i] = base[rand.Intn(4)]
}
dnaStr := string(dnaSeq)
dnaSubseq := make([]byte, 4)
for i := 0; i < 4; i++ {
dnaSubseq[i] = base[rand.Intn(4)]
}
dnaSubstr := string(dnaSubseq)
fmt.Println("DNA sequnence:")
for i := chunkSize; i <= len(dnaStr); i += chunkSize {
start := i - chunkSize
fmt.Printf("%3d..%3d: %s\n", start+1, i, dnaStr[start:i])
}
fmt.Println("\nSubsequence to locate:", dnaSubstr)
var r = regexp.MustCompile(dnaSubstr)
var matches = r.FindAllStringIndex(dnaStr, -1)
if len(matches) == 0 {
fmt.Println("No matches found.")
} else {
fmt.Println("Matches found at the following indices:")
for _, m := range matches {
fmt.Printf("%3d..%-3d\n", m[0]+1, m[1])
}
}
}
func main() {
rand.Seed(time.Now().UnixNano())
findDnaSubsequence(200, 20)
fmt.Println()
findDnaSubsequence(600, 40)
}</syntaxhighlight>
{{out}}
Sample run:
<pre>
DNA sequnence:
1.. 20: GTTGCCCACACGTCTTATTG
21.. 40: TAAAAATCACCGTGCAGCGA
41.. 60: GGTTAAAAATGGTAGGAAAA
61.. 80: TATCCTCAGCCAGCGGTGCC
81..100: GGCCAACAAAAGGGACGTTG
101..120: GATTAAAGTAGGTCTAGGTA
121..140: TCTCGTATCCGGTTGATCCG
141..160: GGATGGTGGACGATATTGGA
161..180: GACCGGAGTGTACATCGGTG
181..200: TTGTCGCTTGCAGCTACGGT
Subsequence to locate: AATA
Matches found at the following indices:
59..62
DNA sequnence:
1.. 40: GTACAGCCACTGTTAGTAGACGGATGCTATTGGGACGCAA
41.. 80: CACATCAGTACACTGCTTGTTCGTAATCGCGTACCCAGCG
81..120: CAAAAGGAGGGGAGGAACCTGCTCAGACTGTCGCTAAAAA
121..160: CGAGCACGTGTCCTTACGCAGTGATGGTAGCGGTCCACGA
161..200: CTTCCACTGGCATAAGGAGAATGTTTAGTAACGCCCCTCA
201..240: TAGGTGCAATTCTACAGGTTAAGGGACCGTGGGATGTTTC
241..280: TATAAAAGTTGAAGAGATTACTAATCCGTCCCGTGCGCGT
281..320: GCCGCAATTTAGCGCCCGTTCTTGAGTAAACATACATGCA
321..360: CGCTCTTGAGTTTTCTAAAACCTGATCAAAACGGTCGCCC
361..400: ACATGCAGGAGCGCCGCAGGGTTTCAGAGGTCAACCATCG
401..440: GCAGCACACGTGAACCCTCTGTACTGACCAGGGGCTTGCT
441..480: CCTTGGTAGGAGATGGTGGAGAATGCGTCGATGCACTGAA
481..520: GCAGACCGCTGATAGCATGTACGATGTTTACGGGTTGACG
521..560: ATAGCTTTGCTAGTGATCGAACATATGATGAAAAACGCTT
561..600: CCATTGATAGAGCATCTTAGGAGCTCAGTCCAGTGACCTC
Subsequence to locate: AGGT
Matches found at the following indices:
202..205
216..219
388..391
</pre>
=={{header|jq}}==
{{works with|jq}}
'''Works with gojq, the Go implementation of jq'''
Neither jq nor gojq currently has any PRNG built-ins so one
possibility is to use a jq-coded PRNG function such
as can be found at https://rosettacode.org/wiki/Random_numbers#jq
In practice, it's usually more convenient to use a utility such as
gshuf or jot to provide the source of randomness. Here we use
`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:
<syntaxhighlight lang="sh">
# For 200 pseudo-random integers in the range 0 to 3 inclusive:
gshuf -i 0-3 -r -n 200 --random-source=/dev/random
</syntaxhighlight>
Note that the indices shown below are offsets (i.e., the index origin is taken to be 0).
<syntaxhighlight lang="sh">
#!/bin/bash
jot -r 200 0 3 | jq -nr --slurpfile four <(jot -r 4 0 3) '
# input: an array of integers
def toDNA:
def base: . as $in | "ACGT" | .[$in : $in+1];
map(base) | join("");
([inputs] | toDNA) as $strand
| ($four | toDNA) as $four
| "Strand of length \($strand|length):",
$strand,
"Zero-based indices of \($four):",
($strand | indices($four) | join(" "))
'</syntaxhighlight>
{{out}}
<pre>
./bioinformatics-subsequence.sh
Strand of length 200:
TGGGCCCAAGCATTGCCACGTAGCTTTGTCAGTGGGCTTGTAAGGGACGAACACAAACTCACAGACCAGGAATTCTCGAGTTCCAGTCCCCCCACTTGTCGCTATTTAGTTAAGACGTTCAGTTTCGTTGCGAACTGTGTCCCCCAGGCTAACGTGATGGGTGTCAGGAATCAATGGCCAACTTTCAGTTAGACTTGACC
Zero-based indices of CAAC:
178
./bioinformatics-subsequence.sh
Strand of length 200:
TAAGACTGCAGGGTACGAAGAGTGGAAGATTGGCTCGTACTTGTCGACGTCGCGTGACATAATCTCTGTGCTCGCCTCGCAGTAAGGGACTAGGTCCCGTTCGAGCGCCCTGCTAGAAGGAGCATCCTACCATGCTCTGATGACATCCTGTCGGCATTAGAGTTTCTACGACATCTAAAGAGTACGATCGACTTCCCAGT
Zero-based indices of GACA:
55 141 169
</pre>
=={{header|Julia}}==
<
DNAsearch(needle, haystack, lap=true) = findall(needle, haystack, overlap=lap)
Line 83 ⟶ 577:
println("Search sequence:\n$rand_string\nfor substring $subseq. Found at positions: ")
foreach(p -> print(rpad(p[2], 8), p[1] % 10 == 0 ? "\n" : ""), enumerate(DNAsearch(subseq, rand_string)))
</
<pre>
Search sequence:
Line 90 ⟶ 584:
21:24 74:77 99:102
</pre>
=={{header|Nim}}==
<syntaxhighlight lang="nim">import random, sequtils, strutils
proc dnaSequence(n: Positive): string =
## Create a random DNA sequence of length "n".
newSeqWith(n, sample("ACGT")).join()
proc positions(dnaSeq, subSeq: string): seq[int] =
## Return the list of starting positions of a subsequence
## "subSeq" in a sequence "dnaSeq". Positions start at 1.
var start = 0
while true:
let pos = dnaSeq.find(subSeq, start)
if pos < 0: break
result.add pos + 1
start = pos + 1
when isMainModule:
const
N = 200
Step = 20
randomize()
let dnaSeq = dnaSequence(N)
echo "DNA sequence:"
for i in countup(0, N - 1, Step):
echo ($(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(", ")</syntaxhighlight>
{{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>
=={{header|Perl}}==
<syntaxhighlight lang="perl">use strict;
use warnings;
use feature 'say';
my @bases = <A C G T>;
my $basecnt = 160;
my($string,$target);
$string .= $bases[ int rand @bases ] for 1 .. $basecnt;
$target .= $bases[ int rand @bases ] for 1 .. 4;
say "Target: $target";
say 'Matches at these positions:';
say (($string =~ s/.{1,40}\K/\n/gr) =~ s/($target)/ >$1< /gr);</syntaxhighlight>
{{out}}
<pre>Target: CCTG
Matches at these positions:
9
90
157
TTGCC >CCTG< CAAAGTTAATAAGTAAACAATTAAGTGAGTG
CTCTAGGGTAAGGTGAGGGCGGGAAGGGGAAAAATACCGA
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 "<=<==>".
<!--<syntaxhighlight lang="phix">(phixonline)-->
<span style="color: #008080;">with</span> <span style="color: #008080;">javascript_semantics</span>
<span style="color: #008080;">constant</span> <span style="color: #000000;">cheat</span> <span style="color: #0000FF;">=</span> <span style="color: #004600;">false</span>
<span style="color: #008080;">function</span> <span style="color: #000000;">grandna</span><span style="color: #0000FF;">(</span><span style="color: #004080;">integer</span> <span style="color: #000000;">len</span><span style="color: #0000FF;">)</span>
<span style="color: #004080;">string</span> <span style="color: #000000;">dna</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">repeat</span><span style="color: #0000FF;">(</span><span style="color: #008000;">' '</span><span style="color: #0000FF;">,</span><span style="color: #000000;">len</span><span style="color: #0000FF;">)</span>
<span style="color: #008080;">for</span> <span style="color: #000000;">i</span><span style="color: #0000FF;">=</span><span style="color: #000000;">1</span> <span style="color: #008080;">to</span> <span style="color: #000000;">len</span> <span style="color: #008080;">do</span> <span style="color: #000000;">dna</span><span style="color: #0000FF;">[</span><span style="color: #000000;">i</span><span style="color: #0000FF;">]</span> <span style="color: #0000FF;">=</span> <span style="color: #008000;">"ACGT"</span><span style="color: #0000FF;">[</span><span style="color: #7060A8;">rand</span><span style="color: #0000FF;">(</span><span style="color: #000000;">4</span
<span style="color: #008080;">return</span> <span style="color: #000000;">dna</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">function</span>
<span style="color: #008080;">procedure</span> <span style="color: #000000;">show</span><span style="color: #0000FF;">(</span><span style="color: #004080;">string</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: #004080;">sequence</span> <span style="color: #000000;">idx</span><span style="color: #0000FF;">)</span>
<span style="color: #000000;">idx</span> <span style="color: #0000FF;">
<span style="color: #004080;">sequence</span> <span style="color: #000000;">s</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">split</span><span style="color: #0000FF;">(</span><span style="color: #7060A8;">trim</span><span style="color: #0000FF;">(</span><span style="color: #7060A8;">join_by</span><span style="color: #0000FF;">(</span><span style="color: #7060A8;">split</span><span style="color: #0000FF;">(</span><span style="color: #7060A8;">join_by</span><span style="color: #0000FF;">(</span><span style="color: #000000;">dna</span><span style="color: #0000FF;">,</span><span style="color: #000000;">1</span><span style="color: #0000FF;">,</span><span style="color: #000000;">10</span><span style="color: #0000FF;">,</span><span style="color: #008000;">""</span><span style="color: #0000FF;">),</span
<span style="color: #004080;">integer</span> <span style="color: #000000;">ii</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">1</span><span style="color: #0000FF;">,</span> <span style="color: #000080;font-style:italic;">-- idx index</span>
<span style="color: #000000;">i</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">idx</span><span style="color: #0000FF;">[</span><span style="color: #000000;">ii</span
<span style="color: #000000;">ux</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">1</span><span style="color: #0000FF;">,</span> <span style="color: #000080;font-style:italic;">-- underline index (1..4)</span>
<span style="color: #000000;">ldx</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">1</span> <span style="color: #000080;font-style:italic;">-- line index (1, 51, 101, etc)</span>
<span style="color: #008080;">for</span> <span style="color: #000000;">si</span><span style="color: #0000FF;">=</span><span style="color: #000000;">1</span> <span style="color: #008080;">to</span> <span style="color: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">s</span><span style="color: #0000FF;">)</span> <span style="color: #008080;">do</span>
<span style="color: #7060A8;">printf</span><span style="color: #0000FF;">(</span><span style="color: #000000;">1</span><span style="color: #0000FF;">,</span><span style="color: #008000;">"%3d: %s\n"</span><span style="color: #0000FF;">,{</span
<span style="color: #000000;">ldx</span> <span style="color: #0000FF;">+=</span> <span style="color: #000000;">50</span>
<span style="color: #008080;">if</span> <span style="color: #000000;">i</span> <span style="color: #008080;">and</span> <span style="color: #000000;">i</span><span style="color: #0000FF;"><</span><span style="color: #000000;">ldx</span> <span style="color: #008080;">then</span>
<span style="color: #004080;">string</span> <span style="color: #000000;">ul</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">repeat</span><span style="color: #0000FF;">(</span><span style="color: #008000;">' '</span><span style="color: #0000FF;">,</span><span style="color: #000000;">59</span><span style="color: #0000FF;">)</span>
<span style="color: #008080;">while</span> <span style="color: #000000;">i</span> <span style="color: #008080;">and</span> <span style="color: #000000;">i</span><span style="color: #0000FF;"><</span><span style="color: #000000;">ldx</span> <span style="color: #008080;">do</span>
<span style="color: #004080;">integer</span> <span style="color: #000000;">up</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">i</span><span style="color: #0000FF;">-</span><span style="color: #000000;">ldx</span><span style="color: #0000FF;">+</span><span style="color: #000000;">51</span> <span style="color: #000080;font-style:italic;">-- underline pos (relative to ldx)</span>
<span style="color: #000000;">up</span> <span style="color: #0000FF;">+=</span> <span style="color: #7060A8;">floor</span
<span style="color: #000000;">ul</span><span style="color: #0000FF;">[</span><span style="color: #000000;">up</span><span style="color: #0000FF;">]</span> <span style="color: #0000FF;">=</span> <span style="color: #008000;">"
<span style="color: #000000;">ux</span> <span style="color: #0000FF;">+=</span> <span style="color: #000000;">1</span>
<span style="color: #000000;">i</span> <span style="color: #0000FF;">+=</span> <span style="color: #000000;">1</span>
<span style="color: #008080;">if</span> <span style="color: #000000;">ux</span><span style="color: #0000FF;">></span><span style="color: #000000;">4</span> <span style="color: #008080;">then</span>
<span style="color: #000000;">ux</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">1</span>
<span style="color: #000000;">ii</span> <span style="color: #0000FF;">+=</span> <span style="color: #000000;">1</span>
<span style="color: #000000;">i</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">idx</span><span style="color: #0000FF;">[</span><span style="color: #000000;">ii</span><span style="color: #0000FF;">]</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">if</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">while</span>
<span style="color: #7060A8;">printf</span><span style="color: #0000FF;">(</span><span style="color: #000000;">1</span><span style="color: #0000FF;">,</span><span style="color: #008000;">"%s\n"</span><span style="color: #0000FF;">,</span><span style="color: #000000;">ul</span><span style="color: #0000FF;">)</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">if</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">for</span>
<span style="color: #008080;">if</span> <span style="color: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">idx</span><span style="color: #0000FF;">)></span><span style="color: #000000;">1</span> <span style="color: #008080;">then</span>
<span style="color: #004080;">string</span> <span style="color: #000000;">
<span style="color: #000000;">t</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">join</span><span style="color: #0000FF;">(</span><span style="color: #7060A8;">apply</span><span style="color: #0000FF;">(</span><span style="color: #000000;">idx</span><span style="color: #0000FF;">
<span style="color: #7060A8;">printf</span><span style="color: #0000FF;">(</span><span style="color: #000000;">1</span><span style="color: #0000FF;">,</span><span style="color: #008000;">"%s occurs at location%s: %s\n"</span
<span style="color: #008080;">else</span>
<span style="color: #7060A8;">printf</span><span style="color: #0000FF;">(</span><span style="color: #000000;">1</span><span style="color: #0000FF;">,</span><span style="color: #008000;">"%s does not occur\n"</span
<span style="color: #008080;">end</span> <span style="color: #008080;">if</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">procedure</span>
<span style="color: #
<span style="color: #008080;">constant</span> <span style="color: #000000;">cheats</span> <span style="color: #0000FF;">=</span> <span style="color: #008080;">iff</span><span style="color: #0000FF;">(</span><span style="color: #000000;">cheat</span><span style="color: #0000FF;">?{</span><span style="color: #000000;">9</span><span style="color: #0000FF;">,</span><span style="color: #000000;">13</span><span style="color: #0000FF;">,</span><span style="color: #000000;">49</span><span style="color: #0000FF;">,</span><span style="color: #000000;">60</span><span style="color: #0000FF;">,</span><span style="color: #000000;">64</span><span style="color: #0000FF;">,</span><span style="color: #000000;">68</span><span style="color: #0000FF;">}:{})</span>
<span style="color: #008080;">for</span> <span style="color: #000000;">i</span><span style="color: #
<span style="color: #000000;">dna</span><span style="color: #0000FF;">[</span><span style="color: #000000;">cheats</span><span style="color: #0000FF;">[</span><span style="color: #000000;">i</span><span style="color: #0000FF;">]..</span><span style="color: #000000;">cheats</span><span style="color: #0000FF;">[</span><span style="color: #000000;">i</span><span style="color: #0000FF;">]+</span><span style="color: #000000;">3</span><span style="color: #0000FF;">]</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">test</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">for</span>
<span style="color: #004080;">sequence</span> <span style="color: #000000;">idx</span> <span style="color: #0000FF;">=</span> <span style="color: #
<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>
<!--</
{{out}}
with cheat enabled
Line 181 ⟶ 744:
GCTA does not occur
</pre>
=={{header|Python}}==
{{works with|Python|3.8}}
{{libheader|regex}}
<syntaxhighlight lang="python">
from random import choice
import regex as re
import time
def generate_sequence(n: int ) -> str:
return "".join([ choice(['A','C','G','T']) for _ in range(n) ])
def dna_findall(needle: str, haystack: str) -> None:
if sum(1 for _ in re.finditer(needle, haystack, overlapped=True)) == 0:
print("No matches found")
else:
print(f"Found {needle} at the following indices: ")
for match in re.finditer(needle, haystack, overlapped=True):
print(f"{match.start()}:{match.end()} ")
dna_seq = generate_sequence(200)
sample_seq = generate_sequence(4)
c = 1
for i in dna_seq:
print(i, end="") if c % 20 != 0 else print(f"{i}")
c += 1
print(f"\nSearch Sample: {sample_seq}")
dna_findall(sample_seq, dna_seq)
</syntaxhighlight>
{{out}}
<pre>
TTGCCCCTGTACTGAGCCCA
TAAGCTTGCACTCAAGGTTT
TGCCCCCTCATATTATAACG
CATCCATTATACAAAACCGA
TACCCTTCCGCATATTATGA
AAAGTGGCGAAGTGCCTTGA
TTTGCATTCATAGTACAACG
GTGCAAAAGCATTGTATGTC
TCACATTTACATGGGAAATG
CCTAGTAGGTGCAAGACCTG
Search Sample: TACA
Found TACA at the following indices:
69:73
133:137
167:171
</pre>
=={{header|Racket}}==
<syntaxhighlight lang="racket">#lang racket
(define (rand-seq n)
(build-string n (lambda _ (string-ref "TGAC" (random 4)))))
(define (subsequence-indices full part)
(let ((part-length (string-length part)) (full-length (string-length full)))
(for/list ((i (- full-length part-length))
#:when (for/and ((p part) (f (in-string full i))) (eq? p f)))
(cons i (+ i part-length -1)))))
(define (report-sequence s (l 50))
(string-join (for/list ((i (in-range 0 (string-length s) l)))
(format "~a: ~a" (~a #:width 4 i)
(substring s i (min (string-length s) (+ i l)))))
"\n"))
(define (Bioinformatics/Subsequence (full (rand-seq 400)) (sub (rand-seq 4)))
(printf "Indices of ~a in~%~a~%~a~%"
sub (report-sequence full) (subsequence-indices full sub)))
(module+ main (for ((i 4)) (Bioinformatics/Subsequence)))</syntaxhighlight>
{{out}}
<pre>Indices of TTAC in
0 : TTATCCTACCGCGTAAGTTCAATGCTCACCGCAGTTTGCTAACCGTTCCT
50 : AAATTCACTTCCTAAGGTATCTTTCGCTTAATTGATGCCGATTGAATTCC
100 : ACGGAGGGCGTAATTGTTTCGGACTTTAGACCTGACATAAGGGCACACTA
150 : GTCCTATTGAATTTGGTGCTATTCGGCGACCTACTAACCTTAGTCAGTGA
200 : AGAGCCATCTCAAAAGTACAGTCATCCTCAAGTGTTACATACGGCACCAT
250 : GACAGTGTATAAGCATGGAGGTTGGCCTATCGTCATATCGAGGCGGCGCC
300 : ATAGACCGGCCAGGTGATGAGATCGACTTTAATGTTGTTGCTTAGCTTGA
350 : CCTCTAGTTTGGATTAAGACGGTCATAGATAGATAGACCGTAAAGTATTC
((234 . 237))
Indices of GTAA in
0 : GTCAGTCCACGCAAGAATAGCAGTTGAGTGGACAATTTATGAGACGGAGA
50 : TAAGTAACCCGCTCCGAGATAAACGTCAGCCGGATTCCGCTGAGTCGGTC
100 : GCCTTCCAAGTGGCAGCTTGTTTGCATTGCTTACAGTGACTTGAACGATC
150 : ACCTACTCGAGGACTCTGCGGGTATTCCAGTTGCCTTGCACTCAGCGATG
200 : CACAAACTTTAAATTATCACAGAAAGAATGTGATTCGGGTGGTCACCCTT
250 : ATCGGTGAAACCAGTCCTTCCATGGGCATATTCTGCGTCGAAATGAGCCC
300 : GCTGTTTACGTTGTACGAACTGGGGACCTAAGGAAACGGGCCGTTCTTAG
350 : GTGATGTCAGCTGCAACGAACTACTGTTAACCTTCTCGATCTGTTGAAAA
((53 . 56))
Indices of AACG in
0 : TTTACAGTACGATTCCGAAGACACAAGAATGCGCCGGCTGTGGGTAGGGG
50 : CGACCCTGCGCGACCTATAAAAGGGGCGACTCAATTTTAGGCCCACCACG
100 : GACCCAGCCCTGTGCACAGAGCGGGGCATTTTTACCTCGCGTGCGCACCA
150 : ACTGCGATCTGCCTTGTCACATAATCCCACATACGAGTTGTATCTCTAAG
200 : AAGGGATGAGGCCAATTTAAATCCGGGTGCATTTCTCGGGGGGAGACACC
250 : AATGAGAGTGGGGCAAGGTGGCGTAGAGAGCTAATCGGGTTTTATGACCG
300 : CGGAAGACCTGGGATACGTCTGGGTGATAACTGAGGGCAGGTCAACGAAC
350 : CCTGATGCGTAGCCACGTCTCAGCTATCGGGCCTGTTTTCATAGTCCATG
((343 . 346))
Indices of CAGC in
0 : TGTGAACCACTATGACACGCTACACGCCTCAAGTTGGCCCCCATATAAGA
50 : ATATCCATCGGTTAATGTGTCTCGCGGCCGTTAGAACAAGCACTAAAGTT
100 : AGAGAAACCAACCATTGGACTAGATCAACATCAACGTCGCTGATAATAAA
150 : TGTATATCTGATGTGGCCGTTCATAAAATCGTTAACTACAGGTATCAACA
200 : TAGTCTCCCAACTTATATAATTGGTTAACTTAGGAGGAGCTTGCACAGCT
250 : CAGCTATATGCTATCTGGCCCTGGGCTTGGTAGGCATCACGTCGTTATGC
300 : TGCGAACATCTCAAAGACAAACGTTGATCCAGCCCCTAGAGAGGTCATTA
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.
<syntaxhighlight lang="raku"
my $line = 80;
Line 205 ⟶ 886:
}
say $disp;</
{{out}}
Show in custom div to better display highlighting.
Line 234 ⟶ 915:
:* DNA proteins to be searched in the data (the default is four unique random proteins).
:* the seed for the RANDOM function so runs can be repeated with the same data (no default).
<
parse arg totLen rndLen basePr oWidth Bevery rndDNA seed .
if totLen=='' | totLen=="," then totLen= 200 /*Not specified? Then use the default.*/
Line 279 ⟶ 960:
end /*j*/
if $\=='' then say right(idx, 7)"│" strip($, 'T') /*show residual protein data*/
say
say; return</syntaxhighlight>
{{out|output|text= when using the default inputs:}}
<pre>
Line 286 ⟶ 968:
1│ TTTTTAGCG CGTTTTGTAG CGCTCTAAAA ACCGTAGCTA TATTTCTCGA AGTTTCACCC AGCTCTTTTG CCCCAGGGTT GCGCTAAGCC CAGCTTCGAG
101│ GGGGCACAG GTAAAATACT ACCGTCCGTG GAGGGGGATG AATTGACCCG ACATTTTTTG AAGCATAACT CGTGACTCAA TATTGCATGA TTACACCAGC
───────┴──────────────────────────────────────────────────────────────────────────────────────────────────────────────
base DNA proteins used: ACGT
Line 307 ⟶ 990:
801│ CCTATCAGT CCAATCCCAC GGGGAGGGCA CTCGCGCAAT TCATTCAAAG AGGGCCATTT GCCGATATAA GGTCCATCAT CGGGAGGAAT ATGACTCCTG
901│ TTAGTATTA GAGCAGCCTC GCTGCGTACT ACTGTCAGTG GCCCGTCAGG GAAGGCAAAA CGTTTTTCCT CTAGGAATCC GTCAATTGGA CTTCTAGACT
───────┴──────────────────────────────────────────────────────────────────────────────────────────────────────────────
base DNA proteins used: ACGT
Line 313 ⟶ 997:
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
Line 563 ⟶ 1,246:
//-----------------------------------------
</syntaxhighlight>
'''Output:'''
[https://i.imgur.com/5hhbRBK.mp4 Bioinformatics/Subsequence - video]
=={{header|Wren}}==
{{libheader|Wren-pattern}}
{{libheader|Wren-str}}
{{libheader|Wren-fmt}}
<
import "./pattern" for Pattern
import "./str" for Str
import "./fmt" for Fmt
var rand = Random.new()
Line 605 ⟶ 1,291:
findDnaSubsequence.call(200, 20)
System.print()
findDnaSubsequence.call(600, 40)</
{{out}}
| |||