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
Randomly generate a string of 200 DNA bases (represented by A, C, G, and T).
Write a routine to find all the positions of a randomly generated subsequence (four letters).
11l[edit]
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)- Output:
GAAGTGCTCAAACCCTTTTT CCTTGCCGTAGGTTGTGCTG CCGCCGCACACCCGCAACAG CTTTTAGGCATAAGTATACG GACCGCGGACGGGGCGTAAC GGTGAACATTTTGCTAAATT GGCTCTAGGGATGAGCCCTA TAGCGCTGGGGACTACGCCC CGGTAAAGATCGAGGCGACT CACCGATTGCGCTAGGGACA Search Sample: CGTA Found CGTA at the following indices: 26:30 94:98
Action![edit]
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- Output:
Screenshot from Atari 8-bit computer
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
Ada[edit]
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;
- Output:
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
Arturo[edit]
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
]
- Output:
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
Factor[edit]
USING: accessors formatting grouping io kernel math
math.functions.integer-logs math.parser random regexp sequences ;
: new-dna ( n -- str ) [ "ACGT" random ] "" replicate-as ;
: pad ( n d -- str ) [ number>string ] dip 32 pad-head ;
:: .dna ( seq n -- )
seq length integer-log10 1 + :> d seq n group
[ n * d pad write ": " write write nl ] each-index ;
: .match ( slice -- ) [ from>> ] [ to>> ] bi "%d..%d\n" printf ;
: .matches ( slices -- )
"Matches found at the following indices:" print
[ .match ] each ;
: .locate ( slices -- )
[ "No matches found." print ] [ .matches ] if-empty ;
: .biosub ( dna-size row-size -- )
[ new-dna dup ] [ .dna nl ] bi*
4 new-dna dup "Subsequence to locate: %s\n" printf
<regexp> all-matching-slices .locate ;
80 10 .biosub nl
600 39 .biosub nl
- Output:
0: ATTCAAGGAC 10: CACTATTAAC 20: CTGCATTGTG 30: AGAACTTGCA 40: GTGTACCGAG 50: AGCGAGTTTA 60: AAGCAACACA 70: TCTTTACCGA Subsequence to locate: GTAG No matches found. 0: GATCTCGTCATGGTCCATCCTAACATTTCGGTTGTGGGC 39: GCATCCCGATAGGCGAAGTTAAATCTACGTAGTCCTACG 78: TCACGACGGAACATGATTGCCCACCGAAGTCGTAGGCGA 117: GCTAAAGTCGGTACATACACGATCTGCTATATTCGTTCT 156: CCGACACACGACATGCAATCCGAGAAGCTCTCGAAGTGC 195: GGTCAGATCCTCAGACTCGAACAGAGGAGACCTTAACTG 234: ATACCCACAGTACTTCTCGCATAACCTAAGCACCTATGC 273: TTACACCATCGTCCTGATATTGAGTGAGTCTGGTCGGAG 312: ATATTATCTAGCACCCTCAAGCTCTGTGTGCCACACCAG 351: GATTCCACTTCGCGCTTGCCTAGAGAAAGTAGAGTAGGT 390: GGTGTCATTAGTACACTGTTTGCGATGCACCAACCAAAC 429: CCGACCGCCATGATGACTGCTTTTCGGCCAACGTCAGAT 468: TAAGAGTACTTTTAGTAGCACCGCAAGCCAGCCGGTTTA 507: GCAAGATCCTGCAGCCTCCACGTTATTTCAGGTCTCTAA 546: GCGTTCTTTCCATGGAAGTAGTCACCGCTCCCGTTGCCA 585: ATGGACACAGACGTT Subsequence to locate: ATAT Matches found at the following indices: 145..149 289..293 312..316
Go[edit]
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)
}
- Output:
Sample run:
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
jq[edit]
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:
# For 200 pseudo-random integers in the range 0 to 3 inclusive:
gshuf -i 0-3 -r -n 200 --random-source=/dev/random
Note that the indices shown below are offsets (i.e., the index origin is taken to be 0).
#!/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($four) | join(" "))
'
- Output:
./bioinformatics-subsequence.sh Strand of length 200: TGGGCCCAAGCATTGCCACGTAGCTTTGTCAGTGGGCTTGTAAGGGACGAACACAAACTCACAGACCAGGAATTCTCGAGTTCCAGTCCCCCCACTTGTCGCTATTTAGTTAAGACGTTCAGTTTCGTTGCGAACTGTGTCCCCCAGGCTAACGTGATGGGTGTCAGGAATCAATGGCCAACTTTCAGTTAGACTTGACC Zero-based indices of CAAC: 178 ./bioinformatics-subsequence.sh Strand of length 200: TAAGACTGCAGGGTACGAAGAGTGGAAGATTGGCTCGTACTTGTCGACGTCGCGTGACATAATCTCTGTGCTCGCCTCGCAGTAAGGGACTAGGTCCCGTTCGAGCGCCCTGCTAGAAGGAGCATCCTACCATGCTCTGATGACATCCTGTCGGCATTAGAGTTTCTACGACATCTAAAGAGTACGATCGACTTCCCAGT Zero-based indices of GACA: 55 141 169
Julia[edit]
DNArand(n, bases=['A', 'T', 'C', 'G']) = String(rand(bases, n))
DNAsearch(needle, haystack, lap=true) = findall(needle, haystack, overlap=lap)
const rand_string = DNArand(200)
const subseq = DNArand(4)
println("Search sequence:\n$rand_string\nfor substring $subseq. Found at positions: ")
foreach(p -> print(rpad(p[2], 8), p[1] % 10 == 0 ? "\n" : ""), enumerate(DNAsearch(subseq, rand_string)))
- Output:
Search sequence: CCGAAGCCAGGAGGACTGAGCGCTTGCGTCCCGAGTTCTGCGACGAGTCTCTTCATTATAAGGCCACTGATTGCGCTCATCATGAGTGCCAGAAGCACCGCTAAACATAAGTGTCCTTTCTTCCTGACGCACTTGAAGATTGTGACCATTTGTGCGGGTTGTGAGTTAGGGGCTCTCATTGTACACGATCTATAGTGTGC for substring CGCT. Found at positions: 21:24 74:77 99:102
Nim[edit]
import random, sequtils, strutils
proc dnaSequence(n: Positive): string =
## Create a random DNA sequence of length "n".
newSeqWith(n, sample("ACGT")).join()
proc positions(dnaSeq, subSeq: string): seq[int] =
## Return the list of starting positions of a subsequence
## "subSeq" in a sequence "dnaSeq". Positions start at 1.
var start = 0
while true:
let pos = dnaSeq.find(subSeq, start)
if pos < 0: break
result.add pos + 1
start = pos + 1
when isMainModule:
const
N = 200
Step = 20
randomize()
let dnaSeq = dnaSequence(N)
echo "DNA sequence:"
for i in countup(0, N - 1, Step):
echo ($(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(", ")
- Output:
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
Perl[edit]
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)/ >$1< /gr);
- Output:
Target: CCTG Matches at these positions: 9 90 157 TTGCC >CCTG< CAAAGTTAATAAGTAAACAATTAAGTGAGTG CTCTAGGGTAAGGTGAGGGCGGGAAGGGGAAAAATACCGA TGCGAG >CCTG< TAGAGCCGGGCCTCAAATTAAACGAAAAAT ATAAGTTTGCTTGGCACGCTGTACTACTTATCC >CCTG< ACT
Phix[edit]
Currently only searches for non-overlapped sequences, but it should be pretty obvious how to change that, in which case the next underline will simply partially overwrite the previous, so you'll get eg "<=<==>".
with javascript_semantics constant cheat = false function grandna(integer len) string dna = repeat(' ',len) for i=1 to len do dna[i] = "ACGT"[rand(4)] end for return dna end function procedure show(string dna, test, sequence idx) idx = deep_copy(idx) & length(dna)+100 -- (add an otherwise unused sentinel) sequence s = split(trim(join_by(split(join_by(dna,1,10,""),"\n"),1,5," ")),"\n") integer ii = 1, -- idx index i = idx[ii], -- current target ux = 1, -- underline index (1..4) ldx = 1 -- line index (1, 51, 101, etc) for si=1 to length(s) do printf(1,"%3d: %s\n",{ldx,s[si]}) ldx += 50 if i and i<ldx then string ul = repeat(' ',59) while i and i<ldx do integer up = i-ldx+51 -- underline pos (relative to ldx) up += floor((up-1)/10)+5 -- (plus any needed spacing) ul[up] = "<==>"[ux] ux += 1 i += 1 if ux>4 then ux = 1 ii += 1 i = idx[ii] end if end while printf(1,"%s\n",ul) end if end for if length(idx)>1 then string p = iff(length(idx)>1?"s":""), t = join(apply(idx[1..$-1],sprint),", ") printf(1,"%s occurs at location%s: %s\n",{test,p,t}) else printf(1,"%s does not occur\n",{test}) end if end procedure string dna = grandna(200), test = grandna(4) constant cheats = iff(cheat?{9,13,49,60,64,68}:{}) for i=1 to length(cheats) do dna[cheats[i]..cheats[i]+3] = test end for sequence idx = match_all(test,dna) show(dna,test,idx)
- Output:
with cheat enabled
1: GGAGATATCG ACCGACCGAA GTAAAGTCAA AGTCGTCCAA TCCACGGACG
<= =><==> <=
51: ACTTCAGCAC GACCGACCGA CCTATTTAAG AGACCACACT TAAGGAATCC
=> < ==><==><== >
101: ATGCGAAATA AAAATGGGCG AGTAGCCGTG GGGCGCTAAA GCACCCACCT
151: AGTTTTCGCC GAAGTACTAG ACCACCTTCG GATCGACAAA GCTTTCACCA
<==>
CGAC occurs at locations: 9, 13, 49, 60, 64, 68, 184
with cheat disabled
1: TGATTTAAAC CGTGGTGCAA TTTATAAACA CTGCGATATG CCTCCTGATG 51: GCATGGTATT CGACACCAAG ACGCTGGTGG GCACACTGGC TTTCAGAATA 101: GGAGTCACAA TCCCTCTATG ATGTCCTCTA GCGGGTGTGT GTTCAGTGCC 151: AGCGCTTACT TCCGGCGTGG CCGACTCTTT TTAAAGCGTA TAGCTGGGGT GCTA does not occur
Python[edit]
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)
- Output:
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
Racket[edit]
#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)))
- Output:
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))
Raku[edit]
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.
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;
- 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[edit]
This REXX version allows the user to specify:
- length of the (random) DNA data sequence (default is 200).
- length of the (random) DNA sequence (default is four).
- DNA proteins to be used in the sequence (default is ACGT).
- width of the output lines of (random DNA) (default is 100).
- often (if ever) to add a blank to the output (default is every 10 proteins).
- 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).
/*REXX pgm gens random DNA (ACGT) sequence & finds positions of a random 4─protein seq. */
parse arg totLen rndLen basePr oWidth Bevery rndDNA seed .
if totLen=='' | totLen=="," then totLen= 200 /*Not specified? Then use the default.*/
if rndLen=='' | rndLen=="," then rndLen= 4 /* " " " " " " */
if basePr=='' | basePr=="," then basePr= 'acgt' /* " " " " " " */
if oWidth=='' | oWidth=="," then oWidth= 100 /* " " " " " " */
if Bevery=='' | Bevery=="," then Bevery= 10 /* " " " " " " */
if rndDNA=='' | rndDNA=="," then rndDNA= copies(., rndLen) /*what we're looking for*/
if datatype(seed, 'W') then call random ,,seed /*used to generate repeatable random #s*/
call genRnd /*gen data field of random proteins. */
call show /*show " " " " " */
say ' base DNA proteins used: ' basePr
say 'random DNA proteins used: ' dna?
call findRnd
if @=='' then do; say "the random DNA proteins weren't found."; exit 4; end
say 'the random DNA proteins were found in positions:' strip(@)
exit 0 /*stick a fork in it, we're all done. */
/*──────────────────────────────────────────────────────────────────────────────────────*/
commas: parse arg ?; do jc=length(?)-3 to 1 by -3; ?=insert(',', ?, jc); end; return ?
/*──────────────────────────────────────────────────────────────────────────────────────*/
findRnd: @=; p=0 /*@: list of the found target proteins*/
do until p==0; p= pos(dna?, $$, p+1); if p>0 then @= @ commas(p)
/*Found one? Append it to the "Found"s*/
end /*p*/; return
/*──────────────────────────────────────────────────────────────────────────────────────*/
genRnd: dna?=; use= basePr; upper use basePr rndDNA; lenB= length(basePr)
do k=1 for rndLEN; x= substr(rndDNA, k, 1)
if x==. then do; ?= random(1, length(use) ); x= substr(use, ?, 1)
use= delstr(use, ?, 1) /*elide so no protein repeats*/
end
dna?= dna? || x /*build a random protein seq.*/
end /*k*/
return
/*──────────────────────────────────────────────────────────────────────────────────────*/
show: say " index │"center('DNA sequence of ' commas(totLen) " proteins", oWidth+10)
say "───────┼"center('' , oWidth+10, '─')
$=; $$=; idx= 1 /*gen data field of random proteins.*/
do j=1 for totLen; c= substr( basePr, random(1, lenB), 1)
$$= $$ || c /*append a random protein. */
if Bevery\==0 then if j//Bevery==0 then $= $' ' /*possibly add a blank. */
if length( space($ || c, 0) )<oWidth then do; $= $ || c; iterate; end
say strip( right(idx, 7)'│' $, 'T'); $= /*display line ──► terminal.*/
idx= idx + oWidth /*bump the index number. */
end /*j*/
if $\=='' then say right(idx, 7)"│" strip($, 'T') /*show residual protein data*/
say "───────┴"center('' , oWidth+10, '─')
say; return
- output when using the default inputs:
index │ DNA sequence of 200 proteins
───────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────
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
random DNA proteins used: GCAT
the random DNA proteins were found in positions: 162 184
- output when using the inputs of: 1000 , , , , tttt
index │ DNA sequence of 1,000 proteins
───────┼──────────────────────────────────────────────────────────────────────────────────────────────────────────────
1│ GTGATTTTT AGCGCGTTTT GTAGCGCTCT AAAAACCGTA GCTATATTTC TCGAAGTTTC ACCCAGCTCT TTTGCCCCAG GGTTGCGCTA AGCCCAGCTT
101│ GAGGGGGGC ACAGGTAAAA TACTACCGTC CGTGGAGGGG GATGAATTGA CCCGACATTT TTTGAAGCAT AACTCGTGAC TCAATATTGC ATGATTACAC
201│ AGCTAGGTT AGTGTAAAAA CCCCCCTATC TTCCTGATCA ATGGCGAGTA AAACATGCAA CCAATTTGTG AGCGAGTACT GGAAATTATT GTTTACGGGA
301│ AGGCACATG CTACGCGCAA CAGATATCTT AGACTGACCC TTTTAGAGTC ATAAGCCCCT GTCGCCTACA TGCTACTAAT ACTCCAACTA GCGGCGCACC
401│ TCAACCGGA TCATGGCGCC AGGGAAAATG TGGCGTAGCG ACGTGCTCAT CGCTCGCCGG GGAGAGCCTT TCAGAATCTC GAATAAAACC TGGTAATGAC
501│ TCATCAATC GTAATGGTCG TCTGGGGCAA GAAGCCGATA TTATAGACTC AGGTCAGACG TGTGCACAAC GGCAGAATTT ATAGTAATTC GCGTGAACTA
601│ GTTTCGGGA TAGGCCTACG ACCAATCATA GGACATTCGA TGCACGGTGT AGAAACAGTT CTCTGATGTT ACTCGGGATA ACACTCGCAA TCCCCTAGGA
701│ ACCGTGAGC GTCGCTAGTA TCTGAGATAG TCGCGACTGC CCAGCGGTCT TTAAGTTCGC ACACTACGGG ACTCCTAGTT CGCCCATTCA TGGCTATTTT
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
random DNA proteins used: TTTT
the random DNA proteins were found in positions: 5 6 16 69 157 158 159 340 796 797 962 963
Ring[edit]
/*-----------------------------------
# Project : DNA subsequences
# Date : 2021/03/23
# Author : Gal Zsolt (~ CalmoSoft ~)
# Email : <calmosoft@gmail.com>
-----------------------------------*/
//-----------------------------------------
load "stdlibcore.ring"
load "guilib.ring"
start = 0
base = ["A","C","G","T"]
dnaList = []
dnaSeq = []
ColLine = list(21)
C_Spacing = 2
C_ButtonDnaStyle = ' background-color: Red; border-radius: 8px;'
C_ButtonStyle = '"background-color:white"; border-radius: 8px;'
Button = newlist(10,20)
LayoutButtonRow = list(10)
//-----------------------------------------
app = new qApp
{
win = new qWidget() {
setWindowTitle('DNA subsequences')
setWinIcon(self,AppFile("white.jpg"))
setStyleSheet('background-color:White')
setgeometry(560,180,300,300)
//reSize(400,400)
winheight = 10
fontSize = 8 # + (winheight / 100)
LayoutButtonMain = new QVBoxLayout()
LayoutButtonMain.setSpacing(C_Spacing)
LayoutButtonMain.setContentsmargins(0,0,0,0)
LabelInd = new qLabel(win) { settext(" DNA subsequences start positions:")
setAlignment(Qt_AlignHCenter | Qt_AlignVCenter)
setStyleSheet("background-color:yellow") }
ButtonInd = new QPushButton(win) { setStyleSheet("background-color:yellow") }
LabelFind = new qLabel(win) { settext(" DNA subsequence to find:")
setStyleSheet("background-color:yellow") }
ButtonFind = new QPushButton(win)
DnaSearch = new QPushButton(win) { setclickevent("pstart()")
setStyleSheet("background-color:yellow")
settext("Find")
}
for Col = 1 to 21
ColLine[Col] = new qLabel(win) {
setmaximumheight(20)
setAlignment(Qt_AlignHCenter | Qt_AlignVCenter)
setStyleSheet("background-color:darkgray")
setText(string(Col-1))
}
next
LayoutInd = new QHBoxLayout() { setSpacing(C_Spacing) setContentsMargins(0,0,0,0) }
LayoutInd.AddWidget(LabelInd)
LayoutInd.AddWidget(ButtonInd)
LayoutButtonMain.AddLayout(LayoutInd)
LayoutTitleRow = new QHBoxLayout() { setSpacing(C_Spacing) setContentsMargins(0,0,0,0) }
for Col = 1 to 21
LayoutTitleRow.AddWidget(ColLine[Col])
next
LayoutButtonMain.AddLayout(LayoutTitleRow)
RowLine = list(10)
for Row = 1 to 10
Letter = "" + Row*20
if Row*20 < 100
Letter = " " + Row*20
ok
RowLine[Row] = new qLabel(win) { setFont(new qFont("Verdana",fontSize,40,0))
setAlignment(Qt_AlignHCenter | Qt_AlignVCenter)
setStyleSheet("background-color:darkgray")
setText(Letter)
}
next
for Row = 1 to 10
LayoutButtonRow[Row] = new QHBoxLayout()
{
setSpacing(C_Spacing)
setContentsmargins(0,0,0,0)
}
LayoutButtonRow[Row].AddWidget(RowLine[Row])
for Col = 1 to 20
Button[Row][Col] = new QPushButton(win) {
setmaximumwidth(20)
}
LayoutButtonRow[Row].AddWidget(Button[Row][Col])
next
LayoutButtonMain.AddLayout(LayoutButtonRow[Row])
next
LayoutDataRow = new QHBoxLayout() { setSpacing(C_Spacing) setContentsMargins(0,0,0,0) }
LayoutDataRow.AddWidget(LabelFind)
LayoutDataRow.AddWidget(ButtonFind)
LayoutDataRow.AddWidget(DnaSearch)
LayoutButtonMain.AddLayout(LayoutDataRow)
setLayout(LayoutButtonMain)
pStart()
show()
}
exec()
}
//-----------------------------------------
func pStart()
start = start + 1
dnaList = []
for row = 1 to 10
for col = 1 to 20
Button[row][col].settext("")
next
next
for nr = 1 to 200
rnd = random(3)+1
baseStr = base[rnd]
row = ceil(nr/20)
col = nr%20
if col = 0
col = 20
ok
Button[row][col].settext(baseStr)
add(dnaList,baseStr)
next
startDna()
//-----------------------------------------
func startDna()
strDna = list2str(dnaList)
strDna = substr(strDna,nl,"")
while true
strBase = ""
for n = 1 to 4
rnd = random(3)+1
strBase = strBase + base[rnd]
next
ind = substr(strDna,strBase)
if ind > 0
exit
ok
end
showDna(dnaList)
//-----------------------------------------
func showDna(dnaList)
if start > 1
see nl
for n = 1 to len(dnaSeq)
for m = 0 to 3
ind = dnaSeq[n] + m
row = ceil(ind/20)
col = ind%20
if col = 0
col = 20
ok
Button[row][col].setstylesheet(C_ButtonStyle)
next
next
ok
dnaSeq = []
strDna = list2str(dnaList)
strDna = substr(strDna,nl,"")
while true
strBase = ""
for n = 1 to 4
rnd = random(3)+1
strBase = strBase + base[rnd]
next
ind = substr(strDna,strBase)
if ind > 0
exit
ok
end
ButtonFind.setStyleSheet("background-color:yellow")
ButtonFind.settext(strBase)
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
add(dnaSeq,n)
ok
next
temp = ""
ButtonInd.settext("")
for nr = 1 to len(dnaList)
ind = find(dnaSeq,nr)
if ind > 0
temp = temp + string(dnaSeq[ind]) + " "
ButtonInd.settext(temp)
for n = nr to nr + 3
row = ceil(n/20)
col = n%20
if col = 0
col = 20
ok
Button[row][col].setStyleSheet(C_ButtonDnaStyle)
Button[row][col].settext(dnaList[n])
next
ok
next
//-----------------------------------------Output:
Bioinformatics/Subsequence - video
Wren[edit]
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)
- 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