Bioinformatics/Subsequence: Difference between revisions
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GCTA does not occur
</pre>
=={{header|Python}}==
{{works with|Python|3.8}}
{{libheader|regex}}
<lang python>
from random import choice
import regex as re
import time
def generate_sequence(n: int ) -> list:
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)
</lang>
{{out}}
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
=={{header|Raku}}==
|
Revision as of 20:28, 27 March 2021
- 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).
Factor
<lang factor>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</lang>
- 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
Julia
<lang julia>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)))
</lang>
- Output:
Search sequence: CCGAAGCCAGGAGGACTGAGCGCTTGCGTCCCGAGTTCTGCGACGAGTCTCTTCATTATAAGGCCACTGATTGCGCTCATCATGAGTGCCAGAAGCACCGCTAAACATAAGTGTCCTTTCTTCCTGACGCACTTGAAGATTGTGACCATTTGTGCGGGTTGTGAGTTAGGGGCTCTCATTGTACACGATCTATAGTGTGC for substring CGCT. Found at positions: 21:24 74:77 99:102
Perl
<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);</lang>
- Output:
Target: CCTG Matches at these positions: 9 90 157 TTGCC >CCTG< CAAAGTTAATAAGTAAACAATTAAGTGAGTG CTCTAGGGTAAGGTGAGGGCGGGAAGGGGAAAAATACCGA TGCGAG >CCTG< TAGAGCCGGGCCTCAAATTAAACGAAAAAT ATAAGTTTGCTTGGCACGCTGTACTACTTATCC >CCTG< ACT
Phix
Note: match_all() is due to become a builtin in the next release, so the version below may or may not need renaming/deleting before it will run.
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 "<=<==>".
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, sequence idx) 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) then string s = iff(length(idx)>1?"s":""), t = join(apply(idx,sprint),", ") printf(1,"%s occurs at location%s: %s\n",{test,s,t}) else printf(1,"%s does not occur\n",{test}) end if end procedure function match_all(object needle, sequence haystack, bool bOverlap = false) if atom(needle) then return find_all(needle,haystack) end if integer start = 1 sequence res = {} while 1 do start = match(needle,haystack,start) if start=0 then exit end if res = append(res,start) start += iff(bOverlap?1:length(needle)) end while return res end function 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