Bioinformatics/Sequence mutation: Difference between revisions
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* Give more information on the individual mutations applied.
* Allow mutations to be weighted and/or chosen.
=={{header|11l}}==
{{trans|Python}}
<syntaxhighlight lang="11l">UInt32 seed = 0
F nonrandom(n)
:seed = 1664525 * :seed + 1013904223
R Int(:seed >> 16) % n
F nonrandom_choice(lst)
R lst[nonrandom(lst.len)]
F basecount(dna)
DefaultDict[Char, Int] d
L(c) dna
d[c]++
R sorted(d.items())
F seq_split(dna, n = 50)
R (0 .< dna.len).step(n).map(i -> @dna[i .< i + @n])
F seq_pp(dna, n = 50)
L(part) seq_split(dna, n)
print(‘#5: #.’.format(L.index * n, part))
print("\n BASECOUNT:")
V tot = 0
L(base, count) basecount(dna)
print(‘ #3: #.’.format(base, count))
tot += count
V (base, count) = (‘TOT’, tot)
print(‘ #3= #.’.format(base, count))
F seq_mutate(String =dna; count = 1, kinds = ‘IDSSSS’, choice = ‘ATCG’)
[(String, Int)] mutation
V k2txt = [‘I’ = ‘Insert’, ‘D’ = ‘Delete’, ‘S’ = ‘Substitute’]
L 0 .< count
V kind = nonrandom_choice(kinds)
V index = nonrandom(dna.len + 1)
I kind == ‘I’
dna = dna[0 .< index]‘’nonrandom_choice(choice)‘’dna[index..]
E I kind == ‘D’ & !dna.empty
dna = dna[0 .< index]‘’dna[index+1..]
E I kind == ‘S’ & !dna.empty
dna = dna[0 .< index]‘’nonrandom_choice(choice)‘’dna[index+1..]
mutation.append((k2txt[kind], index))
R (dna, mutation)
print(‘SEQUENCE:’)
V sequence = ‘TCAATCATTAATCGATTAATACATTCAATTTGAACATCTCCAGGAGAAGGCAGGGTAATCTCGTGTAGCCGTGCTTGGGGCCTCCGATATGGCCGGGGAATTTCAAAGTATAGTGTGCATCCCCTCATAATACATAGATCTATAGGTAAGTATATGGGTTGACGTTGTTAGATGCGATACACGTGCACACTTTATGAATTTTACGTTCCTCTGCCTAGAGTGCCAAGTTTCAATTTGCTACGGTTCCTCA’
seq_pp(sequence)
print("\n\nMUTATIONS:")
V (mseq, m) = seq_mutate(sequence, 10)
L(kind, index) m
print(‘ #10 @#.’.format(kind, index))
print()
seq_pp(mseq)</syntaxhighlight>
{{out}}
<pre>
SEQUENCE:
0: TCAATCATTAATCGATTAATACATTCAATTTGAACATCTCCAGGAGAAGG
50: CAGGGTAATCTCGTGTAGCCGTGCTTGGGGCCTCCGATATGGCCGGGGAA
100: TTTCAAAGTATAGTGTGCATCCCCTCATAATACATAGATCTATAGGTAAG
150: TATATGGGTTGACGTTGTTAGATGCGATACACGTGCACACTTTATGAATT
200: TTACGTTCCTCTGCCTAGAGTGCCAAGTTTCAATTTGCTACGGTTCCTCA
BASECOUNT:
A: 66
C: 51
G: 55
T: 78
TOT= 250
MUTATIONS:
Substitute @184
Substitute @70
Substitute @28
Substitute @6
Substitute @25
Substitute @197
Substitute @81
Substitute @130
Substitute @76
Delete @76
0: TCAATCTTTAATCGATTAATACATTCAATTTGAACATCTCCAGGAGAAGG
50: CAGGGTAATCTCGTGTAGCCCTGCTTGGGCATCCGATATGGCCGGGGAAT
100: TTCAAAGTATAGTGTGCATCCCCTCATAACACATAGATCTATAGGTAAGT
150: ATATGGGTTGACGTTGTTAGATGCGATACACGTACACACTTTATGATTTT
200: TACGTTCCTCTGCCTAGAGTGCCAAGTTTCAATTTGCTACGGTTCCTCA
BASECOUNT:
A: 66
C: 52
G: 52
T: 79
TOT= 249
</pre>
=={{header|Ada}}==
<syntaxhighlight lang="ada">with Ada.Containers.Vectors;
with Ada.Numerics.Discrete_Random;
with Ada.Text_Io;
procedure Mutations is
Width : constant := 60;
type Nucleotide_Type is (A, C, G, T);
type Operation_Type is (Delete, Insert, Swap);
type Position_Type is new Natural;
package Position_Io is new Ada.Text_Io.Integer_Io (Position_Type);
package Nucleotide_Io is new Ada.Text_Io.Enumeration_Io (Nucleotide_Type);
package Operation_Io is new Ada.Text_Io.Enumeration_Io (Operation_Type);
use Ada.Text_Io, Position_Io, Nucleotide_Io, Operation_Io;
package Sequence_Vectors is new Ada.Containers.Vectors (Index_Type => Position_Type,
Element_Type => Nucleotide_Type);
package Nucleotide_Generators is new Ada.Numerics.Discrete_Random (Result_Subtype => Nucleotide_Type);
package Operation_Generators is new Ada.Numerics.Discrete_Random (Result_Subtype => Operation_Type);
procedure Pretty_Print (Sequence : Sequence_Vectors.Vector) is
First : Position_Type := Sequence.First_Index;
Last : Position_Type;
Count : array (Nucleotide_Type) of Natural := (others => 0);
begin
Last := Position_Type'Min (First + Width - 1,
Sequence.Last_Index);
loop
Position_Io.Put (First, Width => 4);
Put (": ");
for N in First .. Last loop
declare
Nucleotide : Nucleotide_Type renames Sequence (N);
begin
Put (Nucleotide);
Count (Nucleotide) := Count (Nucleotide) + 1;
end;
end loop;
New_Line;
exit when Last = Sequence.Last_Index;
First := Last + 1;
Last := Position_Type'Min (First + Width - 1,
Sequence.Last_Index);
end loop;
for N in Count'Range loop
Put ("Count of "); Put (N); Put (" is "); Put (Natural'Image (Count (N))); New_Line;
end loop;
end Pretty_Print;
function Random_Position (First, Last : Position_Type) return Position_Type is
subtype Position_Range is Position_Type range First .. Last;
package Position_Generators is new Ada.Numerics.Discrete_Random (Result_Subtype => Position_Range);
Generator : Position_Generators.Generator;
begin
Position_Generators.Reset (Generator);
return Position_Generators.Random (Generator);
end Random_Position;
Nucleotide_Generator : Nucleotide_Generators.Generator;
Operation_Generator : Operation_Generators.Generator;
Sequence : Sequence_Vectors.Vector;
Position : Position_Type;
Nucleotide : Nucleotide_Type;
Operation : Operation_Type;
begin
Nucleotide_Generators.Reset (Nucleotide_Generator);
Operation_Generators.Reset (Operation_Generator);
for A in 1 .. 200 loop
Sequence.Append (Nucleotide_Generators.Random (Nucleotide_Generator));
end loop;
Put_Line ("Initial sequence:");
Pretty_Print (Sequence);
New_Line;
Put_Line ("Mutations:");
for Mutate in 1 .. 10 loop
Operation := Operation_Generators.Random (Operation_Generator);
case Operation is
when Delete =>
Position := Random_Position (Sequence.First_Index, Sequence.Last_Index);
Sequence.Delete (Index => Position);
Put (Operation); Put (" at position "); Put (Position, Width => 0); New_Line;
when Insert =>
Position := Random_Position (Sequence.First_Index, Sequence.Last_Index + 1);
Nucleotide := Nucleotide_Generators.Random (Nucleotide_Generator);
Sequence.Insert (Before => Position,
New_Item => Nucleotide);
Put (Operation); Put (" "); Put (Nucleotide); Put (" at position ");
Put (Position, Width => 0); New_Line;
when Swap =>
Position := Random_Position (Sequence.First_Index, Sequence.Last_Index);
Nucleotide := Nucleotide_Generators.Random (Nucleotide_Generator);
Sequence.Replace_Element (Index => Position,
New_Item => Nucleotide);
Put (Operation); Put (" at position "); Put (Position, Width => 0);
Put (" to "); Put (Nucleotide); New_Line;
end case;
end loop;
New_Line;
Put_Line ("Mutated sequence:");
Pretty_Print (Sequence);
end Mutations;</syntaxhighlight>
{{out}}
<pre>Initial sequence:
0: GCTGAGTCCGAATTAGTATTCATGAGATACGCATGTCAGTACGGCGACGACACGGGAAGA
60: GCAGATGAAAACTACTGGGGAGCTACCGAGCTGCCGTCGATTGTACGGATGTTATATTTC
120: CCATAGAACTACGAAGTTTTAGGATCCTTTCGGCGATGTGATAAGCAGGTATCAGTAGTA
180: AGCGAAGCGTTGACGTTTTT
Count of A is 55
Count of C is 37
Count of G is 56
Count of T is 52
Mutations:
DELETE at position 129
SWAP at position 172 to T
SWAP at position 28 to T
INSERT A at position 193
DELETE at position 164
SWAP at position 165 to G
DELETE at position 91
INSERT A at position 169
INSERT C at position 72
DELETE at position 146
Mutated sequence:
0: GCTGAGTCCGAATTAGTATTCATGAGATTCGCATGTCAGTACGGCGACGACACGGGAAGA
60: GCAGATGAAAACCTACTGGGGAGCTACCGAGCGCCGTCGATTGTACGGATGTTATATTTC
120: CCATAGAACACGAAGTTTTAGGATCCTTCGGCGATGTGATAAGAGGTATACTGTAGTAAG
180: CGAAGCGTTGACAGTTTTT
Count of A is 55
Count of C is 37
Count of G is 56
Count of T is 51</pre>
=={{header|Arturo}}==
<syntaxhighlight lang="rebol">bases: ["A" "T" "G" "C"]
dna: map 1..200 => [sample bases]
prettyPrint: function [in][
count: #[ A: 0, T: 0, G: 0, C: 0 ]
loop.with:'i split.every:50 in 'line [
prints [pad to :string i*50 3 ":"]
print map split.every:10 line => join
loop split line 'ch [
case [ch=]
when? -> "A" -> count\A: count\A + 1
when? -> "T" -> count\T: count\T + 1
when? -> "G" -> count\G: count\G + 1
when? -> "C" -> count\C: count\C + 1
else []
]
]
print ["Total count => A:" count\A, "T:" count\T "G:" count\G "C:" count\C]
]
performRandomModifications: function [seq,times][
result: new seq
loop times [x][
what: random 1 3
case [what=]
when? -> 1 [
ind: random 0 (size result)
previous: get result ind
next: sample bases
set result ind next
print ["changing base at position" ind "from" previous "to" next]
]
when? -> 2 [
ind: random 0 (size result)
next: sample bases
result: insert result ind next
print ["inserting base" next "at position" ind]
]
else [
ind: random 0 (size result)
previous: get result ind
result: remove result .index ind
print ["deleting base" previous "at position" ind]
]
]
return result
]
print "------------------------------"
print " Initial sequence"
print "------------------------------"
prettyPrint dna
print ""
print "------------------------------"
print " Modifying sequence"
print "------------------------------"
dna: performRandomModifications dna 10
print ""
print "------------------------------"
print " Final sequence"
print "------------------------------"
prettyPrint dna
print ""</syntaxhighlight>
{{out}}
<pre>------------------------------
Initial sequence
------------------------------
0 : GGCCGAAGGC GGCATCAGTG GACTGGGTTG TGGAGCAAAA CGAACACGCC
50 : GAGAGCCGGA GGGTTCGGAA GATTTATTTA GGACGAAATC CCGGACATGT
100 : CGCCCTAGAT TGGCCTCCCT ACACCTAGTA TTATTACTCC TACGCGTTTG
150 : CCTACTGGGT GTCATCTCGT GTTAATCGCA AAATCACCTA CGAATTGCCC
Total count => A: 48 T: 47 G: 53 C: 52
------------------------------
Modifying sequence
------------------------------
deleting base A at position 180
changing base at position 110 from T to G
inserting base T at position 104
inserting base C at position 180
changing base at position 183 from A to A
deleting base C at position 90
changing base at position 6 from A to T
inserting base C at position 146
inserting base G at position 4
changing base at position 150 from T to C
------------------------------
Final sequence
------------------------------
0 : GGCCGGATGG CGGCATCAGT GGACTGGGTT GTGGAGCAAA ACGAACACGC
50 : CGAGAGCCGG AGGGTTCGGA AGATTTATTT AGGACGAAAT CCGGACATGT
100 : CGCCTCTAGA TGGGCCTCCC TACACCTAGT ATTATTACTC CTACGCGCTT
150 : CGCCTACTGG GTGTCATCTC GTGTTAATCG CCAAATCACC TACGAATTGC
200 : CC
Total count => A: 46 T: 47 G: 55 C: 54</pre>
=={{header|BBC BASIC}}==
{{works with|BBC BASIC for Windows}}
<syntaxhighlight lang="bbcbasic"> Mutations = 10
InitialLength = 400
@%=3
REM Generate sequence and Pretty Print result.
FOR I%=1 TO InitialLength
Sequence$ += FNRandomBase
NEXT
PROCDisplaySequence(Sequence$, 50)
REM Make mutations and Pretty Print result.
PRINT '"Mutating..."
FOR I%=1 TO Mutations
Position = RND(LENSequence$)
CurBase$ = MID$(Sequence$, Position, 1)
NewBase$ = FNRandomBase
CASE RND(3) OF
WHEN 1 REM Change a base
PRINT "Change base " CurBase$ " at position " Position " to base " NewBase$
MID$(Sequence$, Position, 1)=NewBase$
WHEN 2 REM Delete a base
PRINT "Delete base " CurBase$ " at position " Position
Sequence$=LEFT$(Sequence$, Position - 1) + MID$(Sequence$, Position + 1)
WHEN 3 REM Insert a base
PRINT "Insert base " NewBase$ " at position " Position
Sequence$=LEFT$(Sequence$, Position) + NewBase$ + MID$(Sequence$, Position + 1)
ENDCASE
NEXT
PROCDisplaySequence(Sequence$, 50)
END
DEF FNRandomBase = MID$("ACGT", RND(4), 1)
DEF PROCDisplaySequence(seq$, snap%)
LOCAL a, c, g, t, i%, p%
p% = !^seq$
FOR i%=0 TO LENseq$ - 1
IF i% MOD snap% == 0 PRINT 'i% ": ";
VDU p%?i%
CASE p%?i% OF
WHEN ASC"A" a += 1
WHEN ASC"C" c += 1
WHEN ASC"G" g += 1
WHEN ASC"T" t += 1
ENDCASE
NEXT
PRINT ' "A: " a ' "C: " c ' "G: " g ' "T: " t
PRINT "Total: "; a + c + g + t
ENDPROC</syntaxhighlight>
{{out}}
<pre>
0: CATGGAAGCTACGTGACTGAGGTACCCGTCGCAGGTTCGAATAAATGATA
50: CTAAAATATCGACGCTAGATACAATATAATGTCTGTAGAAAGCGTCCCTT
100: ATGTTTACATAGGAAAGTATGTGTCGGGCGCCCATGCATTTTCTTAGGCA
150: GCGGAAGCCCCGTGGCGCTCGGCCTCCGCTTTTATTACTTTTAACGTAAC
200: GAGGCGCGGGCGTTGCTTTCTTCCGGCTACCGGCGTCGCACCTAACGCCG
250: GCTGCGAATCGCGCGTTTGTAATTACAAGTTAATTACGATATGCCTCGCA
300: AGTTTTGGCTACCGCTGCCCGGATACTTGGGACGTACGGTATTTCACGCA
350: TCAACAGGTATCCCCCTCCCCTTAGTCTTCCACGACTACTTATTTGAGGG
A: 90
C: 104
G: 97
T: 109
Total: 400
Mutating...
Delete base A at position 69
Change base A at position 154 to base T
Delete base T at position 342
Delete base T at position 83
Insert base G at position 278
Insert base G at position 336
Delete base A at position 48
Insert base T at position 233
Change base T at position 233 to base C
Delete base G at position 148
0: CATGGAAGCTACGTGACTGAGGTACCCGTCGCAGGTTCGAATAAATGTAC
50: TAAAATATCGACGCTAGTACAATATAATGTCGTAGAAAGCGTCCCTTATG
100: TTTACATAGGAAAGTATGTGTCGGGCGCCCATGCATTTTCTTAGGCACGG
150: TAGCCCCGTGGCGCTCGGCCTCCGCTTTTATTACTTTTAACGTAACGAGG
200: CGCGGGCGTTGCTTTCTTCCGGCTACCGGCGCTCGCACCTAACGCCGGCT
250: GCGAATCGCGCGTTTGTAATTACAAGTGTAATTACGATATGCCTCGCAAG
300: TTTTGGCTACCGCTGCCCGGATACTTGGGACGTACGGGTATTCACGCATC
350: AACAGGTATCCCCCTCCCCTTAGTCTTCCACGACTACTTATTTGAGGG
A: 87
C: 105
G: 98
T: 108
Total: 398</pre>
=={{header|C}}==
Adenine ( A ) is always swapped for Thymine ( T ) and vice versa. Similarly with Cytosine ( C ) and Guanine ( G ).
<syntaxhighlight lang="c">
#include<stdlib.h>
#include<stdio.h>
Line 230 ⟶ 676:
return 0;
}
</syntaxhighlight>
Sample run :
<pre>
Line 316 ⟶ 762:
Total:513
</pre>
=={{header|C++}}==
<syntaxhighlight lang="cpp">#include <array>
#include <iomanip>
#include <iostream>
#include <random>
#include <string>
class sequence_generator {
public:
sequence_generator();
std::string generate_sequence(size_t length);
void mutate_sequence(std::string&);
static void print_sequence(std::ostream&, const std::string&);
enum class operation { change, erase, insert };
void set_weight(operation, unsigned int);
private:
char get_random_base() {
return bases_[base_dist_(engine_)];
}
operation get_random_operation();
static const std::array<char, 4> bases_;
std::mt19937 engine_;
std::uniform_int_distribution<size_t> base_dist_;
std::array<unsigned int, 3> operation_weight_;
unsigned int total_weight_;
};
const std::array<char, 4> sequence_generator::bases_{ 'A', 'C', 'G', 'T' };
sequence_generator::sequence_generator() : engine_(std::random_device()()),
base_dist_(0, bases_.size() - 1),
total_weight_(operation_weight_.size()) {
operation_weight_.fill(1);
}
sequence_generator::operation sequence_generator::get_random_operation() {
std::uniform_int_distribution<unsigned int> op_dist(0, total_weight_ - 1);
unsigned int n = op_dist(engine_), op = 0, weight = 0;
for (; op < operation_weight_.size(); ++op) {
weight += operation_weight_[op];
if (n < weight)
break;
}
return static_cast<operation>(op);
}
void sequence_generator::set_weight(operation op, unsigned int weight) {
total_weight_ -= operation_weight_[static_cast<size_t>(op)];
operation_weight_[static_cast<size_t>(op)] = weight;
total_weight_ += weight;
}
std::string sequence_generator::generate_sequence(size_t length) {
std::string sequence;
sequence.reserve(length);
for (size_t i = 0; i < length; ++i)
sequence += get_random_base();
return sequence;
}
void sequence_generator::mutate_sequence(std::string& sequence) {
std::uniform_int_distribution<size_t> dist(0, sequence.length() - 1);
size_t pos = dist(engine_);
char b;
switch (get_random_operation()) {
case operation::change:
b = get_random_base();
std::cout << "Change base at position " << pos << " from "
<< sequence[pos] << " to " << b << '\n';
sequence[pos] = b;
break;
case operation::erase:
std::cout << "Erase base " << sequence[pos] << " at position "
<< pos << '\n';
sequence.erase(pos, 1);
break;
case operation::insert:
b = get_random_base();
std::cout << "Insert base " << b << " at position "
<< pos << '\n';
sequence.insert(pos, 1, b);
break;
}
}
void sequence_generator::print_sequence(std::ostream& out, const std::string& sequence) {
constexpr size_t base_count = bases_.size();
std::array<size_t, base_count> count = { 0 };
for (size_t i = 0, n = sequence.length(); i < n; ++i) {
if (i % 50 == 0) {
if (i != 0)
out << '\n';
out << std::setw(3) << i << ": ";
}
out << sequence[i];
for (size_t j = 0; j < base_count; ++j) {
if (bases_[j] == sequence[i]) {
++count[j];
break;
}
}
}
out << '\n';
out << "Base counts:\n";
size_t total = 0;
for (size_t j = 0; j < base_count; ++j) {
total += count[j];
out << bases_[j] << ": " << count[j] << ", ";
}
out << "Total: " << total << '\n';
}
int main() {
sequence_generator gen;
gen.set_weight(sequence_generator::operation::change, 2);
std::string sequence = gen.generate_sequence(250);
std::cout << "Initial sequence:\n";
sequence_generator::print_sequence(std::cout, sequence);
constexpr int count = 10;
for (int i = 0; i < count; ++i)
gen.mutate_sequence(sequence);
std::cout << "After " << count << " mutations:\n";
sequence_generator::print_sequence(std::cout, sequence);
return 0;
}</syntaxhighlight>
{{out}}
<pre>
Initial sequence:
0: CATATCTGCGTAAGGCGTCGAATCCTTAGAGAAAACTCGCCAAACGCGCT
50: AGCCAAGACTTAATTAAAGGCTGGCCACATAACAGTAGTACTGCAAGGAT
100: GACGTGACTACAACGTGGAATACTCTATCTGATGAGCCCCACGTGGGCCA
150: ACCTTCCAATGCGGCGTCTTGCAGTCTTCGGACTTTGCCTCTACTAGGAG
200: TAGCCATGACGAGTGGTGAGGCGGAGGGACCAATTCCGCACTTCGAATCG
Base counts:
A: 67, C: 65, G: 64, T: 54, Total: 250
Change base at position 39 from C to C
Erase base T at position 194
Insert base T at position 70
Insert base C at position 190
Insert base T at position 45
Erase base A at position 111
Change base at position 96 from A to C
Change base at position 113 from A to C
Change base at position 5 from C to A
Change base at position 44 from C to T
After 10 mutations:
0: CATATATGCGTAAGGCGTCGAATCCTTAGAGAAAACTCGCCAAATTGCGC
50: TAGCCAAGACTTAATTAAAGGTCTGGCCACATAACAGTAGTACTGCCAGG
100: ATGACGTGACTCACCGTGGAATACTCTATCTGATGAGCCCCACGTGGGCC
150: AACCTTCCAATGCGGCGTCTTGCAGTCTTCGGACTTTGCCCTCTACAGGA
200: GTAGCCATGACGAGTGGTGAGGCGGAGGGACCAATTCCGCACTTCGAATC
250: G
Base counts:
A: 65, C: 66, G: 64, T: 56, Total: 251
</pre>
=={{header|Common Lisp}}==
<b>Usage :</b>
:(mutate (<i><Genome length> <Number of mutations></i>
:: :ins_w <i><Insertion weight></i> :swp_w <i><Swap weight></i> :del_w <i><Delete weight></i>
:: :genome <i><Genome Sequence></i>)
<b>All keys are optional. <i><Genome length></i> is discarded when :genome is set.</b>
<syntaxhighlight lang="lisp">
(defun random_base ()
(random 4))
(defun basechar (base)
(char "ACTG" base))
(defun generate_genome (genome_length)
(let (genome '())
(loop for i below genome_length do
(push (random_base) genome))
(return-from generate_genome genome)))
(defun map_genome (genome)
(let (seq '())
(loop for n from (1- (length genome)) downto 0 do
(push (position (char genome n) "ACTG") seq))
seq))
(defun output_genome_info (genome &optional (genome_name "ORIGINAL"))
(let ((ac 0) (tc 0) (cc 0) (gc 0))
(format t "~% ---- ~a ----" genome_name)
(do ((n 0 (1+ n)))
((= n (length genome)))
(when (= 0 (mod n 50)) (format t "~& ~4d: " (1+ n)))
(case (nth n genome)
(0 (incf ac))
(1 (incf tc))
(2 (incf cc))
(3 (incf gc)))
(format t "~c" (basechar (nth n genome))))
(format t "~2%- Total : ~3d~%A : ~d C : ~d~%T : ~d G : ~d~2%" (length genome) ac tc cc gc)))
(defun insert_base (genome)
(let ((place (random (length genome)))
(base (random_base)))
(format t "Insert + ~c at ~3d~%"
(basechar base) (+ 1 place))
(if (= 0 place)
(push base genome)
(push base (cdr (nthcdr (1- place) genome))))
(return-from insert_base genome)))
(defun swap_base (genome)
(let ((place (random (length genome)))
(base (random_base)))
(format t "Swap ~c -> ~c at ~3d~%"
(basechar (nth place genome)) (basechar base) (+ 1 place))
(setf (nth place genome) base)
(return-from swap_base genome)))
(defun delete_base (genome)
(let ((place (random (length genome))))
(format t "Delete - ~c at ~3d~%"
(basechar (nth place genome)) (+ 1 place))
(if (= 0 place) (pop genome)
(pop (cdr (nthcdr (1- place) genome))))
(return-from delete_base genome)))
(defun mutate (genome_length n_mutations
&key (ins_w 10) (swp_w 10) (del_w 10)
(genome (generate_genome genome_length) has_genome))
(if has_genome (setf genome (map_genome genome)))
(output_genome_info genome)
(format t " ---- MUTATION SEQUENCE ----~%")
(do ((n 0 (1+ n)))
((= n n_mutations))
(setf mutation_type (random (+ ins_w swp_w del_w)))
(format t "~3d : " (1+ n))
(setf genome
(cond ((< mutation_type ins_w) (insert_base genome))
((< mutation_type (+ ins_w swp_w)) (swap_base genome))
(t (delete_base genome)))))
(output_genome_info genome "MUTATED"))
</syntaxhighlight>
{{out}}
<pre>
[CLISP]> (mutate 500 30 :ins_w 5 :swp_w 10 :del_w 15)
---- ORIGINAL ----
1: CTGCCATGCGTAAGATAGCAGAAGTGTTCGCGTATATGTTCATTTTGGCT
51: TCAACCTACGGGCGTATACACATTTCAGCTCGGAGCTCGGGCCCCAGTAC
101: CTAGTTTTTCTTTCAAGCTGGAACTACGGCGCCTTGTGCCGTAATCCGTC
151: GGGGTGATAATTCTAACTTGCTAACACGCGCAGATGGTCCGGTCGCGGGT
201: CAAACATTCGCCAAGGTCAACTTACCCTTAAAAGGCTTGCAACAGGGACC
251: AGTACTAGGAAGTAGACTTCATGGATCTTGGGCATAGTGGACTAGCTTAT
301: TTACCAGCGACGTTCTTGCACCCGAGACATTATCATAGTTCGACAGCGTT
351: GAACTGTGCTTAGGTTAATGCCGCGCTTCCTACCTTGAACTAAACACAGC
401: ACACAGTGAGAACGTAGCGGCCTCTTTTCCTGCCTGCAATTCGTAAGCCT
451: GATTTGACGGGTCTGGAGTTTGGCTCGGAGTAGGTCTGCTACTTAAATTC
- Total : 500
A : 116 C : 124
T : 137 G : 123
---- MUTATION SEQUENCE ----
1 : Swap T -> C at 74
2 : Delete - T at 208
3 : Insert + C at 332
4 : Insert + G at 287
5 : Delete - T at 188
6 : Swap G -> A at 263
7 : Delete - G at 323
8 : Delete - A at 336
9 : Swap T -> A at 426
10 : Swap G -> G at 38
11 : Swap G -> C at 288
12 : Delete - T at 11
13 : Swap G -> A at 197
14 : Insert + T at 476
15 : Swap C -> A at 5
16 : Swap A -> T at 211
17 : Swap A -> T at 248
18 : Delete - C at 471
19 : Delete - C at 455
20 : Swap T -> T at 184
21 : Insert + T at 224
22 : Delete - T at 224
23 : Insert + T at 333
24 : Delete - C at 18
25 : Delete - G at 139
26 : Delete - T at 333
27 : Insert + T at 80
28 : Insert + T at 480
29 : Swap A -> T at 341
30 : Swap T -> C at 73
---- MUTATED ----
1: CTGCAATGCGAAGATAGAGAAGTGTTCGCGTATATGTTCATTTTGGCTTC
51: AACCTACGGGCGTATACACATCCCAGCTCTGGAGCTCGGGCCCCAGTACC
101: TAGTTTTTCTTTCAAGCTGGAACTACGGCGCCTTGTGCCTAATCCGTCGG
151: GGTGATAATTCTAACTTGCTAACACGCGCAGATGGCCGGTCGCGGATCAA
201: ACATCGCCATGGTCAACTTACCCTTAAAAGGCTTGCAACAGGGACCTGTA
251: CTAGGAAGTAAACTTCATGGATCTTGGGCATAGGTCGACTAGCTTATTTA
301: CCAGCGACGTTCTTGCACCCAGACATTACTCTAGTTCGACTGCGTTGAAC
351: TGTGCTTAGGTTAATGCCGCGCTTCCTACCTTGAACTAAACACAGCACAC
401: AGTGAGAACGTAGCGGCCTCTTTACCTGCCTGCAATTCGTAAGCCTGATT
451: TGAGGGTCTGGAGTTTGGTCGGTAGTAGGTTCTGCTACTTAAATTC
- Total : 496
A : 116 C : 124
T : 137 G : 119
</pre>
=={{header|EasyLang}}==
<syntaxhighlight lang=text>
base$[] = [ "A" "C" "T" "G" ]
global seq[] seqnx[] seqpr[] .
proc prseq . .
len cnt[] 4
numfmt 0 3
ind = 1
while seqnx[ind] <> 1
pos += 1
ind = seqnx[ind]
if pos mod 40 = 1
print ""
.
if pos mod 40 = 1
write pos & ":"
.
if pos mod 4 = 1
write " "
.
cnt[seq[ind]] += 1
write base$[seq[ind]]
.
print ""
print ""
for i to 4
print base$[i] & ":" & cnt[i]
sum += cnt[i]
.
print "====="
print " " & sum
print ""
.
proc init . .
seq[] = [ 0 ]
seqnx[] = [ 2 ]
seqpr[] = [ 0 ]
for i = 2 to 201
seq[] &= random 4
seqnx[] &= i + 1
seqpr[] &= i - 1
.
seqpr[1] = len seq[]
seqnx[$] = 1
.
proc delete pos . .
nx = seqnx[pos]
pre = seqpr[pos]
seqnx[pre] = nx
seqpr[nx] = pre
last = len seq[]
seq[pos] = seq[last]
seqnx[pos] = seqnx[last]
seqpr[pos] = seqpr[last]
seqpr[seqnx[pos]] = pos
seqnx[seqpr[pos]] = pos
len seq[] -1
len seqnx[] -1
len seqpr[] -1
.
proc insert pos . .
seq[] &= random 4
last = len seq[]
seqnx[] &= pos
seqpr[] &= seqpr[pos]
seqnx[seqpr[pos]] = last
seqpr[pos] = last
.
proc mutate . .
op = random 3
pos = random (len seq[] - 1) + 1
if op = 1
seq[pos] = random 4
elif op = 2
insert pos
else
delete pos
.
.
init
print "Original:"
prseq
for i to 10
mutate
.
print "Mutated:"
prseq
</syntaxhighlight>
{{out}}
<pre>
Original:
1: GGCA CGTG TGTA CAAC GCAT CTTT TGTC ATTG CCCT GATC
41: CGCA GTAA CTCC ACAT GCTC GTAC AAAT CGTT ATCT GAGC
81: GCAC GGCC GCCG TGCC AAAA GGAG AAAT CCGA GTAA GTAG
121: CTGA AGTG AGTC GCAT CAAC GTTC ATTA AGAG GAGC GAAA
161: TGTA GGGT AGCT CTTC CTCT TCGT AGTC CCTT ACCG ATGC
A: 50
C: 52
T: 49
G: 49
=====
200
Mutated:
1: GGCA CGTG TGTG CAAC GATC TTTT GTCA TTGC CCTG ATCA
41: CGCA TTAA CTCC ACAT GCTC GTAC AAAT CGTA TCTG AGCG
81: CACG GCCG CCGT GCCA AAAG GAGA ATCC GAGG TAAG TAGC
121: TGAA TGAG TCGC ATCA ACGT TCAT TGAG AGGA GCGA AATG
161: TAGG GTAA CTCT TCCT CTTC GTAG TCCC TTAC CGAT GC
A: 49
C: 51
T: 49
G: 49
=====
198
</pre>
=={{header|Factor}}==
<
macros math math.statistics namespaces prettyprint quotations
random sequences sorting ;
Line 392 ⟶ 1,263:
[ mutate ] curry times nl "MUTATED " write show-dna ;
MAIN: main</
{{out}}
<pre>
Line 439 ⟶ 1,310:
TOTAL: 204
</pre>
=={{header|FreeBASIC}}==
{{trans|Yabasic}}
<syntaxhighlight lang="vb">'' Rosetta Code problem: https://rosettacode.org/wiki/Bioinformatics/Sequence_mutation
'' by Jjuanhdez, 05/2023
Randomize Timer
Dim As Integer r, i
r = Int(Rnd * (300))
Dim Shared As String dnaS
For i = 1 To 200 + r : dnaS += Mid("ACGT", Int(Rnd * (4))+1, 1) : Next
Sub show()
Dim As Integer acgt(4), i, j, x, total
For i = 1 To Len(dnaS)
x = Instr("ACGT", Mid(dnaS, i, 1))
acgt(x) += 1
Next
For i = 1 To 4 : total += acgt(i) : Next
For i = 1 To Len(dnaS) Step 50
Print i; ":"; !"\t";
For j = 0 To 49 Step 10
Print Mid(dnaS, i+j, 10); " ";
Next
Print
Next
Print !"\nBase counts: A:"; acgt(1); ", C:"; acgt(2); ", G:"; acgt(3); ", T:"; acgt(4); ", total:"; total
End Sub
Sub mutate()
Dim As Integer i, p
Dim As String sdiS, repS, wasS
Print
For i = 1 To 10
p = Int(Rnd * (Len(dnaS))) + 1
sdiS = Mid("SDI", Int(Rnd * (3)) + 1, 1)
repS = Mid("ACGT", Int(Rnd * (4)) + 1, 1)
wasS = Mid(dnaS, p, 1)
Select Case sdiS
Case "S"
Mid(dnaS, p, 1) = repS
Print "swapped "; wasS; " at "; p; " for "; repS
Case "D"
dnaS = Left(dnaS, p - 1) + Right(dnaS, Len(dnaS) - p)
Print "deleted "; wasS; " at "; p
Case "I"
dnaS = Left(dnaS, p - 1) + repS + Right(dnaS, (Len(dnaS) - p + 1))
Print "inserted "; repS; " at "; p; ", before "; wasS
End Select
Next
Print
End Sub
show()
mutate()
show()
Sleep</syntaxhighlight>
{{out}}
<pre> 1: GAAATGATTT GTATCGAGCA GACTGGAGAA AGCACTTATT TAAGCACCGT
51: TTCAAAGCCA CTCTGTTAGG AAGCTAATCC GTAGGTACGT AGGGACGACT
101: CGATCGGACC CTTGCTTCGG TGTCTTCGTT CATCCCGGTT TCCGCGCTCA
151: GCTGCATTTT GGTCGAGCCA GGCGATCGAC AATGTTCGAC GCAATAACGC
201: GCCGGATAGG CACCTGGTGT AGTTTAGGCT GTGTCCGCTT CTGCATCTCC
251: GTTTTGAACA ATGAATTTCC ACGCGTCCAA CAGAAAGATT TGCGCCTGTC
301: TGGAGTGGTC GGAACTTAGG TATTCCGTCG TCAGTCGCGC AGAGATCAGC
351: GACCCTCTTG CTCGTGGCCC TGGACGCGTT TCCTCGTTTT AACTCGACAT
401: CCCTGACCAG CATCACTA
Base counts: A: 88, C: 112, G: 106, T: 112, total: 418
swapped T at 246 for C
swapped T at 90 for G
inserted C at 141, before T
deleted T at 62
swapped T at 63 for G
deleted T at 381
deleted T at 389
swapped T at 81 for G
inserted G at 149, before C
swapped T at 256 for T
1: GAAATGATTT GTATCGAGCA GACTGGAGAA AGCACTTATT TAAGCACCGT
51: TTCAAAGCCA CCGGTTAGGA AGCTAATCCG GAGGTACGGA GGGACGACTC
101: GATCGGACCC TTGCTTCGGT GTCTTCGTTC ATCCCGGTTC TCCGCGCTGC
151: AGCTGCATTT TGGTCGAGCC AGGCGATCGA CAATGTTCGA CGCAATAACG
201: CGCCGGATAG GCACCTGGTG TAGTTTAGGC TGTGTCCGCT TCTGCACCTC
251: CGTTTTGAAC AATGAATTTC CACGCGTCCA ACAGAAAGAT TTGCGCCTGT
301: CTGGAGTGGT CGGAACTTAG GTATTCCGTC GTCAGTCGCG CAGAGATCAG
351: CGACCCTCTT GCTCGTGGCC CTGGACGCGT TCCTCGTTTA ACTCGACATC
401: CCTGACCAGC ATCACTA
Base counts: A: 88, C: 114, G: 110, T: 105, total: 417</pre>
=={{header|Go}}==
<
import (
Line 539 ⟶ 1,510:
fmt.Println()
prettyPrint(dna, 50)
}</
{{out}}
Line 594 ⟶ 1,565:
======
</pre>
=={{header|Haskell}}==
<syntaxhighlight lang="haskell">import Data.List (group, sort)
import Data.List.Split (chunksOf)
import System.Random (Random, randomR, random, newStdGen, randoms, getStdRandom)
import Text.Printf (PrintfArg(..), fmtChar, fmtPrecision, formatString, IsChar(..), printf)
data Mutation = Swap | Delete | Insert deriving (Show, Eq, Ord, Enum, Bounded)
data DNABase = A | C | G | T deriving (Show, Read, Eq, Ord, Enum, Bounded)
type DNASequence = [DNABase]
data Result = Swapped Mutation Int (DNABase, DNABase)
| InsertDeleted Mutation Int DNABase
instance Random DNABase where
randomR (a, b) g = case randomR (fromEnum a, fromEnum b) g of (x, y) -> (toEnum x, y)
random = randomR (minBound, maxBound)
instance Random Mutation where
randomR (a, b) g = case randomR (fromEnum a, fromEnum b) g of (x, y) -> (toEnum x, y)
random = randomR (minBound, maxBound)
instance PrintfArg DNABase where
formatArg x fmt = formatString (show x) (fmt { fmtChar = 's', fmtPrecision = Nothing })
instance PrintfArg Mutation where
formatArg x fmt = formatString (show x) (fmt { fmtChar = 's', fmtPrecision = Nothing })
instance IsChar DNABase where
toChar = head . show
fromChar = read . pure
chunkedDNASequence :: DNASequence -> [(Int, [DNABase])]
chunkedDNASequence = zip [50,100..] . chunksOf 50
baseCounts :: DNASequence -> [(DNABase, Int)]
baseCounts = fmap ((,) . head <*> length) . group . sort
newSequence :: Int -> IO DNASequence
newSequence n = take n . randoms <$> newStdGen
mutateSequence :: DNASequence -> IO (Result, DNASequence)
mutateSequence [] = fail "empty dna sequence"
mutateSequence ds = randomMutation >>= mutate ds
where
randomMutation = head . randoms <$> newStdGen
mutate xs m = do
i <- randomIndex (length xs)
case m of
Swap -> randomDNA >>= \d -> pure (Swapped Swap i (xs !! pred i, d), swapElement i d xs)
Insert -> randomDNA >>= \d -> pure (InsertDeleted Insert i d, insertElement i d xs)
Delete -> pure (InsertDeleted Delete i (xs !! pred i), dropElement i xs)
where
dropElement i xs = take (pred i) xs <> drop i xs
insertElement i e xs = take i xs <> [e] <> drop i xs
swapElement i a xs = take (pred i) xs <> [a] <> drop i xs
randomIndex n = getStdRandom (randomR (1, n))
randomDNA = head . randoms <$> newStdGen
mutate :: Int -> DNASequence -> IO DNASequence
mutate 0 s = pure s
mutate n s = do
(r, ms) <- mutateSequence s
case r of
Swapped m i (a, b) -> printf "%6s @ %-3d : %s -> %s \n" m i a b
InsertDeleted m i a -> printf "%6s @ %-3d : %s\n" m i a
mutate (pred n) ms
main :: IO ()
main = do
ds <- newSequence 200
putStrLn "\nInitial Sequence:" >> showSequence ds
putStrLn "\nBase Counts:" >> showBaseCounts ds
showSumBaseCounts ds
ms <- mutate 10 ds
putStrLn "\nMutated Sequence:" >> showSequence ms
putStrLn "\nBase Counts:" >> showBaseCounts ms
showSumBaseCounts ms
where
showSequence = mapM_ (uncurry (printf "%3d: %s\n")) . chunkedDNASequence
showBaseCounts = mapM_ (uncurry (printf "%s: %3d\n")) . baseCounts
showSumBaseCounts xs = putStrLn (replicate 6 '-') >> printf "Σ: %d\n\n" (length xs)</syntaxhighlight>
{{out}}
<pre>Initial Sequence:
50: CCGGCGAACTGGTAGGTCTTTAATTATGCGGCCGCGATCGCGACACAGGT
100: GCAGGAGGAAAATAGGCCCCCGTTCTGGGCAGCCTGATTGCACACTCCCG
150: ATACCAGACGTGTGGCGGCTTTTTCGCAAGATCTTACCAAACATTAAGAT
200: TCGAAATACCAACTGTCGAAAGCAGAACGTGAATGTACCACCCGGATGCG
Base Counts:
A: 53
C: 53
G: 53
T: 41
------
Σ: 200
Insert @ 104 : C
Delete @ 133 : T
Insert @ 60 : A
Insert @ 42 : G
Swap @ 14 : A -> C
Insert @ 88 : A
Delete @ 9 : C
Swap @ 185 : A -> G
Insert @ 27 : G
Swap @ 102 : C -> T
Mutated Sequence:
50: CCGGCGAATGGTCGGTCTTTAATTATGGCGGCCGCGATCGCGGACACAGG
100: TGCAGGAGGAAAAATAGGCCCCCGTTCTGGGCAGCCTGAATTGCACACTC
150: CTGATACCCAGACGTGTGGCGGCTTTTTCGCAAGACTTACCAAACATTAA
200: GATTCGAAATACCAACTGTCGAAAGCAGAACGTGAGTGTACCACCCGGAT
250: GCG
Base Counts:
A: 53
C: 53
G: 56
T: 41
------
Σ: 203</pre>
=={{header|J}}==
<
MUTS=: ;: 'del ins mut'
Line 631 ⟶ 1,722:
)
simulate=: (sim@(1 1 1&; &. |. ))`sim@.(3=#)</
{{out}}
Line 723 ⟶ 1,814:
│ │ 200│GGC │
└─────┴────┴──────────────────────────────────────────────────┘</pre>
=={{header|Java}}==
<p>
This example use a <code>List</code> to hold the base values.<br />
The <code>Random</code> class is used to generate random integer values.<br />
A <code>record</code> is used to hold the counts of each base.
</p>
<p>
The "pretty print" is defined within the <code>toString</code> method.<br />
Which uses a <code>StringBuilder</code> to generate a <kbd>string</kbd> of sequential bases.<br />
A <code>BufferedReader</code> to read the augmented <kbd>string</kbd> line-for-line.<br />
Finally, a <kbd>string</kbd> formatter is used to justify and format the output text.
</p>
<syntaxhighlight lang="java">
import java.io.BufferedReader;
import java.io.IOException;
import java.io.StringReader;
import java.util.ArrayList;
import java.util.List;
import java.util.Random;
class Program {
List<Character> sequence;
Random random;
SequenceMutation() {
sequence = new ArrayList<>();
random = new Random();
}
void generate(int amount) {
for (int count = 0; count < amount; count++)
sequence.add(randomBase());
}
void mutate(int amount) {
int index;
for (int count = 0; count < amount; count++) {
index = random.nextInt(0, sequence.size());
switch (random.nextInt(0, 3)) {
case 0 -> sequence.set(index, randomBase());
case 1 -> sequence.remove(index);
case 2 -> sequence.add(index, randomBase());
}
}
}
private char randomBase() {
return switch (random.nextInt(0, 4)) {
case 0 -> 'A';
case 1 -> 'C';
case 2 -> 'G';
case 3 -> 'T';
default -> '?';
};
}
private Base count(String string) {
int a = 0, c = 0, g = 0, t = 0;
for (char base : string.toCharArray()) {
switch (base) {
case 'A' -> a++;
case 'C' -> c++;
case 'G' -> g++;
case 'T' -> t++;
}
}
return new Base(a, c, g, t);
}
/* used exclusively for count totals */
private record Base(int a, int c, int g, int t) {
int total() {
return a + c + g + t;
}
@Override
public String toString() {
return "[A %2d, C %2d, G %2d, T %2d]".formatted(a, c, g, t);
}
}
@Override
public String toString() {
StringBuilder string = new StringBuilder();
StringBuilder stringB = new StringBuilder();
String newline = System.lineSeparator();
for (int index = 0; index < sequence.size(); index++) {
if (index != 0 && index % 50 == 0)
string.append(newline);
string.append(sequence.get(index));
stringB.append(sequence.get(index));
}
try {
BufferedReader reader = new BufferedReader(new StringReader(string.toString()));
string = new StringBuilder();
int count = 0;
String line;
while ((line = reader.readLine()) != null) {
string.append(count++);
string.append(" %-50s ".formatted(line));
string.append(count(line));
string.append(newline);
}
} catch (IOException exception) {
/* ignore */
}
string.append(newline);
Base bases = count(stringB.toString());
int total = bases.total();
string.append("Total of %d bases%n".formatted(total));
string.append("A %3d (%.2f%%)%n".formatted(bases.a, ((double) bases.a / total) * 100));
string.append("C %3d (%.2f%%)%n".formatted(bases.c, ((double) bases.c / total) * 100));
string.append("G %3d (%.2f%%)%n".formatted(bases.g, ((double) bases.g / total) * 100));
string.append("T %3d (%.2f%%)%n".formatted(bases.t, ((double) bases.t / total) * 100));
return string.toString();
}
}
</syntaxhighlight>
<p>
Here is a sequence of 200 mutated 10 times.
</p>
<pre>
Before mutation
0 TCGCTTGGGGGGAGCAAGGTGTTCGCAATAGATCACAGCCGGTCTCGCAT [A 10, C 12, G 17, T 11]
1 AGCTATTTCTACGCTATCGAGCCTGTACTGTGTCAGTAGACCATGTACTC [A 11, C 13, G 10, T 16]
2 CCCAGACTCGTCTTGCCAAGTGACTGCTCAAGGGGAGCGCCCACAGGGTA [A 11, C 16, G 15, T 8]
3 TCTAGAGCATTCGATCACACGGAAAAATTTTATTCGGCAGATCCAGTTAA [A 17, C 10, G 9, T 14]
Total of 200 bases
A 49 (24.50%)
C 51 (25.50%)
G 51 (25.50%)
T 49 (24.50%)
After mutation
0 TCGCTTGGGGGGAGTAAGGTGTTCGCAATAGTCACAGCCGGTCTCGCATA [A 10, C 11, G 17, T 12]
1 GCTTTTCTACGCATCGAGCCTGTACTGTGTCAGTAGACATGTACTCCCCA [A 10, C 15, G 10, T 15]
2 GACTCGTTTGCCAAGTGACCTGCTCAAGGGGAGCGCCCACAGGGTACTAG [A 11, C 14, G 16, T 9]
3 AGCAGTTCGATCACACGGAAAAATTTTTTCGGCAGATCCAGTTAA [A 15, C 9, G 9, T 12]
Total of 195 bases
A 46 (23.59%)
C 49 (25.13%)
G 52 (26.67%)
T 48 (24.62%)
</pre>
<p>
Here is a sequence of 200 mutated 90,000 times
</p>
<pre>
Before mutation
0 CGCACCCTCCTTCGGGCGAAGCGGGGTTATTTACCCGATTCACCGCACCT [A 8, C 19, G 12, T 11]
1 CGCGGCTCTAAAAGTTCGAAGATCCCTGCGTAGACTGGACCTCATAACAA [A 15, C 14, G 11, T 10]
2 CCGTATTACGCTCCGTACGAATAACTCGGTTGTGCGATGCGGAAAGCGAC [A 12, C 13, G 14, T 11]
3 ATTTCTCAGGCCGAACGTACGCTTCTCTCCTACACCTCGCCTCGAGTATG [A 9, C 18, G 9, T 14]
Total of 200 bases
A 44 (22.00%)
C 64 (32.00%)
G 46 (23.00%)
T 46 (23.00%)
After mutation
0 CGTTTAAGCGGGAAGGTCGTCCACCACACGAAGGCCCCCCTCCAGCACTA [A 12, C 19, G 12, T 7]
1 CCCTGGGCGAGTGCGACCGGCTACAAGAATACGGACAACCGCACTTCGTA [A 13, C 16, G 14, T 7]
2 GTTGCGACGCCAAACCGAGGTTTGAAAGGCAGCCGAAACTCCTAGCCATC [A 14, C 15, G 13, T 8]
3 CGGGCAGCCCACTGGTTTAGATGTTACGTGATGGAAAGGTGGATCATCGT [A 11, C 9, G 17, T 13]
4 GGTTGCCCTGGCGTTGCGTACTTCGTGTCTGAATATTGGTTACAATCGCT [A 7, C 11, G 14, T 18]
5 CGACGACCTGACGATTCTGGATCAACCAACTGCCTAAAGTCGCGAATTAA [A 16, C 14, G 10, T 10]
6 TAATCGACTGCATCACATGTTAGTCTAGTCATCACGAGTACATAGTGTGG [A 14, C 10, G 11, T 15]
7 CCACCTCCTAACGTACTATTTACATAGGATATGGCAGCCCTAACGCACAC [A 15, C 17, G 7, T 11]
8 TGTACGAAAGTGAGACTCCTTACCGAGATTCTAGGCTTAGTGATCCTTGA [A 13, C 10, G 12, T 15]
9 AAACGCTAGCCTAGGAATGACGGGGACTTGATCGGCC [A 10, C 9, G 12, T 6]
Total of 487 bases
A 125 (25.67%)
C 130 (26.69%)
G 122 (25.05%)
T 110 (22.59%)
</pre>
<br />
Here is an alternate demonstration
<syntaxhighlight lang="java">import java.util.Arrays;
import java.util.Random;
public class SequenceMutation {
public static void main(String[] args) {
SequenceMutation sm = new SequenceMutation();
sm.setWeight(OP_CHANGE, 3);
String sequence = sm.generateSequence(250);
System.out.println("Initial sequence:");
printSequence(sequence);
int count = 10;
for (int i = 0; i < count; ++i)
sequence = sm.mutateSequence(sequence);
System.out.println("After " + count + " mutations:");
printSequence(sequence);
}
public SequenceMutation() {
totalWeight_ = OP_COUNT;
Arrays.fill(operationWeight_, 1);
}
public String generateSequence(int length) {
char[] ch = new char[length];
for (int i = 0; i < length; ++i)
ch[i] = getRandomBase();
return new String(ch);
}
public void setWeight(int operation, int weight) {
totalWeight_ -= operationWeight_[operation];
operationWeight_[operation] = weight;
totalWeight_ += weight;
}
public String mutateSequence(String sequence) {
char[] ch = sequence.toCharArray();
int pos = random_.nextInt(ch.length);
int operation = getRandomOperation();
if (operation == OP_CHANGE) {
char b = getRandomBase();
System.out.println("Change base at position " + pos + " from "
+ ch[pos] + " to " + b);
ch[pos] = b;
} else if (operation == OP_ERASE) {
System.out.println("Erase base " + ch[pos] + " at position " + pos);
char[] newCh = new char[ch.length - 1];
System.arraycopy(ch, 0, newCh, 0, pos);
System.arraycopy(ch, pos + 1, newCh, pos, ch.length - pos - 1);
ch = newCh;
} else if (operation == OP_INSERT) {
char b = getRandomBase();
System.out.println("Insert base " + b + " at position " + pos);
char[] newCh = new char[ch.length + 1];
System.arraycopy(ch, 0, newCh, 0, pos);
System.arraycopy(ch, pos, newCh, pos + 1, ch.length - pos);
newCh[pos] = b;
ch = newCh;
}
return new String(ch);
}
public static void printSequence(String sequence) {
int[] count = new int[BASES.length];
for (int i = 0, n = sequence.length(); i < n; ++i) {
if (i % 50 == 0) {
if (i != 0)
System.out.println();
System.out.printf("%3d: ", i);
}
char ch = sequence.charAt(i);
System.out.print(ch);
for (int j = 0; j < BASES.length; ++j) {
if (BASES[j] == ch) {
++count[j];
break;
}
}
}
System.out.println();
System.out.println("Base counts:");
int total = 0;
for (int j = 0; j < BASES.length; ++j) {
total += count[j];
System.out.print(BASES[j] + ": " + count[j] + ", ");
}
System.out.println("Total: " + total);
}
private char getRandomBase() {
return BASES[random_.nextInt(BASES.length)];
}
private int getRandomOperation() {
int n = random_.nextInt(totalWeight_), op = 0;
for (int weight = 0; op < OP_COUNT; ++op) {
weight += operationWeight_[op];
if (n < weight)
break;
}
return op;
}
private final Random random_ = new Random();
private int[] operationWeight_ = new int[OP_COUNT];
private int totalWeight_ = 0;
private static final int OP_CHANGE = 0;
private static final int OP_ERASE = 1;
private static final int OP_INSERT = 2;
private static final int OP_COUNT = 3;
private static final char[] BASES = {'A', 'C', 'G', 'T'};
}</syntaxhighlight>
{{out}}
<pre>
Initial sequence:
0: TCCCCTCCAGTTAGCAGAAATATTAGCTAACGATACCTCGACACGGAGGG
50: GTGGGGCCAACTCTTAACACAATTACGAGAACCATCCTTCGAAAGCAAAA
100: AAGTTTATGCCTGTTGTGTCAGGAACCCCCCGCGACGGACAACACAGTAA
150: GCACCTGCGGATACTGTGGTTGCCCTGAAAGACGGAGGATGCCTCCTATG
200: TCATTTAGAACTATCGAACGTACGGTTCTTAAATGGTCGTAGTTAGATAG
Base counts:
A: 73, C: 61, G: 59, T: 57, Total: 250
Insert base T at position 196
Change base at position 19 from A to G
Erase base T at position 204
Change base at position 223 from G to T
Change base at position 183 from G to C
Change base at position 21 from A to T
Insert base T at position 40
Change base at position 20 from T to G
Insert base T at position 69
Change base at position 19 from G to T
After 10 mutations:
0: TCCCCTCCAGTTAGCAGAATGTTTAGCTAACGATACCTCGTACACGGAGG
50: GGTGGGGCCAACTCTTAACTACAATTACGAGAACCATCCTTCGAAAGCAA
100: AAAAGTTTATGCCTGTTGTGTCAGGAACCCCCCGCGACGGACAACACAGT
150: AAGCACCTGCGGATACTGTGGTTGCCCTGAAAGACCGAGGATGCCTCCTT
200: ATGTCATTAGAACTATCGAACGTACTGTTCTTAAATGGTCGTAGTTAGAT
250: AG
Base counts:
A: 71, C: 62, G: 58, T: 61, Total: 252
</pre>
=={{header|JavaScript}}==
<syntaxhighlight lang="javascript">// Basic set-up
const numBases = 250
const numMutations = 30
const bases = ['A', 'C', 'G', 'T'];
// Utility functions
/**
* Return a shallow copy of an array
* @param {Array<*>} arr
* @returns {*[]}
*/
const copy = arr => [...arr];
/**
* Get a random int up to but excluding the the given number
* @param {number} max
* @returns {number}
*/
const randTo = max => (Math.random() * max) | 0;
/**
* Given an array return a random element and the index of that element from
* the array.
* @param {Array<*>} arr
* @returns {[*[], number]}
*/
const randSelect = arr => {
const at = randTo(arr.length);
return [arr[at], at];
};
/**
* Given a number or string, return a left padded string
* @param {string|number} v
* @returns {string}
*/
const pad = v => ('' + v).padStart(4, ' ');
/**
* Count the number of elements that match the given value in an array
* @param {Array<string>} arr
* @returns {function(string): number}
*/
const filterCount = arr => s => arr.filter(e => e === s).length;
/**
* Utility logging function
* @param {string|number} v
* @param {string|number} n
*/
const print = (v, n) => console.log(`${pad(v)}:\t${n}`)
/**
* Utility function to randomly select a new base, and an index in the given
* sequence.
* @param {Array<string>} seq
* @param {Array<string>} bases
* @returns {[string, string, number]}
*/
const getVars = (seq, bases) => {
const [newBase, _] = randSelect(bases);
const [extBase, randPos] = randSelect(seq);
return [newBase, extBase, randPos];
};
// Bias the operations
/**
* Given a map of function to ratio, return an array of those functions
* appearing ratio number of times in the array.
* @param weightMap
* @returns {Array<function>}
*/
const weightedOps = weightMap => {
return [...weightMap.entries()].reduce((p, [op, weight]) =>
[...p, ...(Array(weight).fill(op))], []);
};
// Pretty Print functions
const prettyPrint = seq => {
let idx = 0;
const rem = seq.reduce((p, c) => {
const s = p + c;
if (s.length === 50) {
print(idx, s);
idx = idx + 50;
return '';
}
return s;
}, '');
if (rem !== '') {
print(idx, rem);
}
}
const printBases = seq => {
const filterSeq = filterCount(seq);
let tot = 0;
[...bases].forEach(e => {
const cnt = filterSeq(e);
print(e, cnt);
tot = tot + cnt;
})
print('Σ', tot);
}
// Mutation definitions
const swap = ([hist, seq]) => {
const arr = copy(seq);
const [newBase, extBase, randPos] = getVars(arr, bases);
arr.splice(randPos, 1, newBase);
return [[...hist, `Swapped ${extBase} for ${newBase} at ${randPos}`], arr];
};
const del = ([hist, seq]) => {
const arr = copy(seq);
const [newBase, extBase, randPos] = getVars(arr, bases);
arr.splice(randPos, 1);
return [[...hist, `Deleted ${extBase} at ${randPos}`], arr];
}
const insert = ([hist, seq]) => {
const arr = copy(seq);
const [newBase, extBase, randPos] = getVars(arr, bases);
arr.splice(randPos, 0, newBase);
return [[...hist, `Inserted ${newBase} at ${randPos}`], arr];
}
// Create the starting sequence
const seq = Array(numBases).fill(undefined).map(
() => randSelect(bases)[0]);
// Create a weighted set of mutations
const weightMap = new Map()
.set(swap, 1)
.set(del, 1)
.set(insert, 1);
const operations = weightedOps(weightMap);
const mutations = Array(numMutations).fill(undefined).map(
() => randSelect(operations)[0]);
// Mutate the sequence
const [hist, mut] = mutations.reduce((p, c) => c(p), [[], seq]);
console.log('ORIGINAL SEQUENCE:')
prettyPrint(seq);
console.log('\nBASE COUNTS:')
printBases(seq);
console.log('\nMUTATION LOG:')
hist.forEach((e, i) => console.log(`${i}:\t${e}`));
console.log('\nMUTATED SEQUENCE:')
prettyPrint(mut);
console.log('\nMUTATED BASE COUNTS:')
printBases(mut);
</syntaxhighlight>
{{out}}
<pre>
ORIGINAL SEQUENCE:
0: GTGATCGTAGCGTATCACACGTGCGGGCAGATTGCGGGGCTTCCGTAAGT
50: CTCTCGATTGGCTAAACCTAACGTATGGAGTCGGGCCTGTTCAGAACTGC
100: GCCATAACCACAAACGTCGACAGATAAAGTTCGTGAAGGGACAGGATGAG
150: ATTTTTTTCCCGGTCTGTGCTCAGGGCTTAAATTAGTGCCTTTCCCGAAT
200: GGATACCAACGATTCTGACTGGTTATTTTAATCACCTAATGCCAGTAGTC
BASE COUNTS:
A: 61
C: 57
G: 64
T: 68
Σ: 250
MUTATION LOG:
0: Inserted A at 231
1: Inserted C at 67
2: Deleted T at 192
3: Inserted A at 106
4: Inserted C at 226
5: Swapped C for G at 34
6: Swapped T for A at 165
7: Inserted G at 11
8: Inserted G at 75
9: Inserted C at 219
10: Swapped A for A at 205
11: Inserted C at 67
12: Inserted C at 34
13: Deleted A at 31
14: Inserted A at 171
15: Deleted G at 0
16: Deleted A at 170
17: Deleted C at 67
18: Deleted T at 173
19: Inserted T at 109
20: Inserted C at 232
21: Inserted G at 137
22: Inserted T at 151
23: Deleted C at 93
24: Deleted A at 95
25: Inserted C at 229
26: Inserted C at 65
27: Inserted G at 84
28: Inserted G at 212
29: Inserted G at 161
MUTATED SEQUENCE:
0: TGATCGTAGCGGTATCACACGTGCGGGCAGTTCGGGGGGCTTCCGTAAGT
50: CTCTCGATTGGCTAACACCCTAACGGTATGGAGTGCGGGCCTGTTAGACT
100: GCGCCATAATACCACAAACGTCGACAGATAAAGTTCGGTGAAGGGACAGG
150: ATTGAGATTTTGTTTCCCGGACTGTGCCAGGGCTTAAATTAGTGCCTTCC
200: CGAATGGATACCAGACGATTCTCGACTGGTTACCTTTCTAAATCACCTAA
250: TGCCAGTAGTC
MUTATED BASE COUNTS:
A: 62
C: 62
G: 70
T: 67
Σ: 261
</pre>
=={{header|jq}}==
{{Works with|jq}}
'''Works with gojq, the Go implementation of jq'''
'''Adapted from [[#Wren|Wren]]'''
Since jq does not include a PRNG, the following assumes that
an external source of entropy such as /dev/urandom is available.
See the "Invocation" section below for details.
<syntaxhighlight lang="jq">
### Generic utilities
# Output: a PRN in range(0; .)
def prn:
if . == 1 then 0
else . as $n
| (($n-1)|tostring|length) as $w
| [limit($w; inputs)] | join("") | tonumber
| if . < $n then . else ($n | prn) end
end;
# bag of words
def bow(stream):
reduce stream as $word ({}; .[($word|tostring)] += 1);
# Emit a stream of the constituent characters of the input string
def chars: explode[] | [.] | implode;
def lpad($len): tostring | ($len - length) as $l | (" " * $l) + .;
# Print $n-character segments at a time, each prefixed by a 1-based index
def pretty_nwise($n):
(length | tostring | length) as $len
| def _n($i):
if length == 0 then empty
else "\($i|lpad($len)): \(.[:$n])",
(.[$n:] | _n($i+$n))
end;
_n(1);
### Biology
def bases: ["A", "C", "G", "T"];
def randomBase:
bases | .[length|prn];
# $w is an array [weightSwap, weightDelete, weightInsert]
# specifying the weights out of 300 for each of swap, delete and insert
# Input: an object {dna}
# Output: an object {dna, message}
def mutate($w):
def removeAt($p): .[:$p] + .[$p+1:];
(.dna|length) as $le
# get a random position in the dna to mutate
| ($le | prn) as $p
# get a random number between 0 and 299 inclusive
| (300 | prn) as $r
| .dna |= [chars]
| if $r < $w[0]
then # swap
randomBase as $base
| .message = " Change @\($p) \(.dna[$p]) to \($base)"
| .dna[$p] = $base
elif $r < $w[0] + $w[1]
then # delete
.message = " Delete @\($p) \(.dna[$p])"
| .dna |= removeAt($p)
else # insert
randomBase as $base
| .message = " Insert @\($p) \($base)"
| .dna |= .[:$p] + [$base] + .[$p:]
end
| .dna |= join("") ;
# Generate a random dna sequence of given length:
def generate($n):
[range(0; $n) | randomBase] | join("");
# Pretty print dna and stats.
def prettyPrint($rowLen):
"SEQUENCE:", pretty_nwise($rowLen),
( bow(chars) as $baseMap
| "\nBASE COUNT:",
( bases[] as $c | " \($c): \($baseMap[$c] // 0)" ),
" ------",
" Σ: \(length)",
" ======\n"
) ;
# For displaying the weights
def pretty_weights:
" Change: \(.[0])\n Delete: \(.[1])\n Insert: \(.[2])";
# Arguments are length, weights, mutations
def task($n; $w; $muts ):
generate($n)
| . as $dna
| prettyPrint(50),
"\nWEIGHTS (0 .. 300):", ($w|pretty_weights),
"\nMUTATIONS (\($muts)):",
(reduce range(0;$muts) as $i ({$dna};
mutate($w)
| .emit += [.message] )
| (.emit | join("\n")),
"",
(.dna | prettyPrint(50)) ) ;
task(250; # length
[100, 100, 100]; # use e.g. [0, 300, 0] to choose only deletions
10 # mutations
)
</syntaxhighlight>
'''Invocation:'''
<pre>
< /dev/urandom tr -cd '0-9' | fold -w 1 | $JQ -cnr -f rc-sequence-mutation.jq
</pre>
{{output}}
<pre>
SEQUENCE:
1: AGGACACTGCCTTATTTTGTTTCAACAGAAGCCATCTCGAGCAACTACGT
51: GGCCACACAAGCTAATACGAATGACCTTGTATGGGGAGTTACGGGGGGTT
101: TATCTTGAGAAATGGTATAACGATACCCCAAGTGGCGTGATAGGCCGCGC
151: GGGCCTCAGAATAGGTCGTAGATCCGTAAGGGCACCGGGAGCCTTTCTTC
201: TCGTATAATCCGCCGAGATGTTAAAAGACAGCTATGGATTCCCGTAATGC
BASE COUNT:
A: 66
C: 57
G: 67
T: 60
------
Σ: 250
======
WEIGHTS (0 .. 300):
Change: 100
Delete: 100
Insert: 100
MUTATIONS (10):
Insert @76 T
Delete @104 C
Change @197 T to T
Insert @206 A
Delete @184 C
Change @69 A to C
Insert @211 G
Delete @31 C
Insert @165 G
Insert @234 T
SEQUENCE:
1: AGGACACTGCCTTATTTTGTTTCAACAGAAGCATCTCGAGCAACTACGTG
51: GCCACACAAGCTAATACGCATGACCTTTGTATGGGGAGTTACGGGGGGTT
101: TATTTGAGAAATGGTATAACGATACCCCAAGTGGCGTGATAGGCCGCGCG
151: GGCCTCAGAATAGGTGCGTAGATCCGTAAGGGCACGGGAGCCTTTCTTCT
201: CGTATAAATCCGGCCGAGATGTTAAAAGACAGCTTATGGATTCCCGTAAT
251: GC
BASE COUNT:
A: 66
C: 55
G: 69
T: 62
------
Σ: 252
======
</pre>
=={{header|Julia}}==
<
randpos(seq) = rand(1:length(seq)) # 1
mutateat(pos, seq) = (s = seq[:]; s[pos] = rand(dnabases); s) # 2-1
Line 778 ⟶ 2,591:
testbioseq()
</
<pre>
500nt DNA sequence:
Line 839 ⟶ 2,652:
</pre>
=={{header|Lua}}==
Using the <code>prettyprint()</code> function from [[Bioinformatics/base_count#Lua]] (not replicated here)
<syntaxhighlight lang="lua">math.randomseed(os.time())
bases = {"A","C","T","G"}
function randbase() return bases[math.random(#bases)] end
function mutate(seq)
local i,h = math.random(#seq), "%-6s %3s at %3d"
local old,new = seq:sub(i,i), randbase()
local ops = {
function(s) h=h:format("Swap", old..">"..new, i) return s:sub(1,i-1)..new..s:sub(i+1) end,
function(s) h=h:format("Delete", " -"..old, i) return s:sub(1,i-1)..s:sub(i+1) end,
function(s) h=h:format("Insert", " +"..new, i) return s:sub(1,i-1)..new..s:sub(i) end,
}
local weighted = { 1,1,2,3 }
local n = weighted[math.random(#weighted)]
return ops[n](seq), h
end
local seq,hist="",{} for i = 1, 200 do seq=seq..randbase() end
print("ORIGINAL:")
prettyprint(seq)
print()
for i = 1, 10 do seq,h=mutate(seq) hist[#hist+1]=h end
print("MUTATIONS:")
for i,h in ipairs(hist) do print(" "..h) end
print()
print("MUTATED:")
prettyprint(seq)</syntaxhighlight>
{{out}}
<pre>ORIGINAL:
LOCUS AB000000 200 bp mRNA linear HUM 01-JAN-2001
BASE COUNT 50 a 47 c 51 g 52 t
ORIGIN
1 atggatccga cgtgattata ttcactatgg ggcaatcgca cattagtttt atctccatca
61 gcgacacgat ggggatcaat gggctgctac tggagacgtc cgatgcgatg attggtaatt
121 gcatagagtg gatctccttt aacctagtag aaacgccctt ccggttcagc atggcgagtg
181 cgtacaacgt cacccagact
MUTATIONS:
Insert +A at 190
Delete -C at 134
Swap A>G at 57
Delete -G at 83
Insert +T at 81
Swap T>T at 164
Delete -C at 199
Swap T>G at 147
Swap C>G at 33
Swap C>G at 191
MUTATED:
LOCUS AB000000 199 bp mRNA linear HUM 01-JAN-2001
BASE COUNT 50 a 43 c 54 g 52 t
ORIGIN
1 atggatccga cgtgattata ttcactatgg gggaatcgca cattagtttt atctccgtca
61 gcgacacgat ggggatcaat tggctgctac tggagacgtc cgatgcgatg attggtaatt
121 gcatagagtg gattccttta acctaggaga aacgcccttc cggttcagca tggcgagtgc
181 gtacaacgat gacccagat</pre>
=={{header|Mathematica}} / {{header|Wolfram Language}}==
BioSequence is a fundamental data type in Mathematica:
<syntaxhighlight lang="mathematica">SeedRandom[13122345];
seq = BioSequence["DNA", "ATAAACGTACGTTTTTAGGCT"];
randompos = RandomInteger[seq["SequenceLength"]];
seq = StringReplacePart[seq, RandomChoice[{"A", "T", "C", "G"}], {randompos, randompos}];
randompos = RandomInteger[seq["SequenceLength"]];
seq = StringReplacePart[seq, "", {randompos, randompos}];
randompos = RandomInteger[seq["SequenceLength"]];
seq = StringInsert[seq, RandomChoice[{"A", "T", "C", "G"}], randompos];
seq = BioSequence["DNA", StringJoin@RandomChoice[{"A", "T", "C", "G"}, 250]];
size = 50;
parts = StringPartition[seq["SequenceString"], UpTo[size]];
begins = Most[Accumulate[Prepend[StringLength /@ parts, 1]]];
ends = Rest[Accumulate[Prepend[StringLength /@ parts, 0]]];
StringRiffle[MapThread[ToString[#1] <> "-" <> ToString[#2] <> ": " <> #3 &, {begins, ends, parts}], "\n"]
Tally[Characters[seq["SequenceString"]]]
Do[
type = RandomChoice[{1, 2, 3}];
Switch[type, 1,
randompos = RandomInteger[seq["SequenceLength"]];
seq = StringReplacePart[seq, RandomChoice[{"A", "T", "C", "G"}], {randompos, randompos}];
, 2,
randompos = RandomInteger[seq["SequenceLength"]];
seq = StringReplacePart[seq, "", {randompos, randompos}];
, 3,
randompos = RandomInteger[seq["SequenceLength"]];
seq = StringInsert[seq, RandomChoice[{"A", "T", "C", "G"}], randompos];
]
,
{10}
]
parts = StringPartition[seq["SequenceString"], UpTo[size]];
begins = Most[Accumulate[Prepend[StringLength /@ parts, 1]]];
ends = Rest[Accumulate[Prepend[StringLength /@ parts, 0]]];
StringRiffle[MapThread[ToString[#1] <> "-" <> ToString[#2] <> ": " <> #3 &, {begins, ends, parts}], "\n"]
Tally[Characters[seq["SequenceString"]]]</syntaxhighlight>
{{out}}
<pre>1-50: TAGCAGGGGAATTGTCGACTCCCGGGTTTCAATTGCCAACCAAGCATATT
51-100: GTACGCTCGTTCATTATAGGGGAAATGCGAGGGGCTAGAACGTTAGCTTC
101-150: GAGAGGTCGCGGCAATTTAGGGGGGCACCAAACGGTTTATAATACAGGGA
151-200: CTGATACATTCGCTGGAAAACAATTCTGCCCAGCAGCGACTCCGGACAAC
201-250: GTGACTTTGGTCCAAGATATTAGATTATCAATCCGTATTAATGTAGGCTT
{{"T", 63}, {"A", 69}, {"G", 66}, {"C", 52}}
1-50: TAGCAGGGGAATTGTCGACTCCCGGGTTCAATTGCCAACCAAGATATTGT
51-100: ACGCTCGTTCATTATAGGGGAAATGCGAGGGGCTAGAAACGTTAGTTCGA
101-150: GAGGTCGCGGAAATTTAGGGGGGCACCAACGGTTTATAATACAGGGACTG
151-200: ATACATTCGCTGGAAAACAATTCTGCCCAGCAGCGACTCCGGACAACGTG
201-246: ACTTTGGTCCAAGATAGTTAGATATCAATCCGTATAATGTAGGCTT
{{"T", 60}, {"A", 70}, {"G", 67}, {"C", 49}}</pre>
=={{header|Nim}}==
<syntaxhighlight lang="nim">import random
import strformat
import strutils
type
# Enumeration type for bases.
Base {.pure.} = enum A, C, G, T, Other = "other"
# Sequence of bases.
DnaSequence = string
# Kind of mutation.
Mutation = enum mutSwap, mutDelete, mutInsert
const MaxBaseVal = ord(Base.high) - 1 # Maximum base value.
#---------------------------------------------------------------------------------------------------
template toChar(base: Base): char = ($base)[0]
#---------------------------------------------------------------------------------------------------
proc newDnaSeq(length: Natural): DnaSequence =
## Create a DNA sequence of given length.
result = newStringOfCap(length)
for _ in 1..length:
result.add($Base(rand(MaxBaseVal)))
#---------------------------------------------------------------------------------------------------
proc mutate(dnaSeq: var DnaSequence) =
## Mutate a sequence (it is changed in place).
# Choose randomly the position of mutation.
let idx = rand(dnaSeq.high)
# Choose randomly the kind of mutation.
let mut = Mutation(rand(ord(Mutation.high)))
# Apply the mutation.
case mut
of mutSwap:
let newBase = Base(rand(MaxBaseVal))
echo fmt"Changing base at position {idx + 1} from {dnaSeq[idx]} to {newBase}"
dnaSeq[idx] = newBase.toChar
of mutDelete:
echo fmt"Deleting base {dnaSeq[idx]} at position {idx + 1}"
dnaSeq.delete(idx, idx)
of mutInsert:
let newBase = Base(rand(MaxBaseVal))
echo fmt"Inserting base {newBase} at position {idx + 1}"
dnaSeq.insert($newBase, idx)
#---------------------------------------------------------------------------------------------------
proc display(dnaSeq: DnaSequence) =
## Display a DNA sequence using EMBL format.
var counts: array[Base, Natural] # Count of bases.
for c in dnaSeq:
inc counts[parseEnum[Base]($c, Other)] # Use Other as default value.
# Display the SQ line.
var sqline = fmt"SQ {dnaSeq.len} BP; "
for (base, count) in counts.pairs:
sqline &= fmt"{count} {base}; "
echo sqline
# Display the sequence.
var idx = 0
var row = newStringOfCap(80)
var remaining = dnaSeq.len
while remaining > 0:
row.setLen(0)
row.add(" ")
# Add groups of 10 bases.
for group in 1..6:
let nextIdx = idx + min(10, remaining)
for i in idx..<nextIdx:
row.add($dnaSeq[i])
row.add(' ')
dec remaining, nextIdx - idx
idx = nextIdx
if remaining == 0:
break
# Append the number of the last base in the row.
row.add(spaces(72 - row.len))
row.add(fmt"{idx:>8}")
echo row
# Add termination.
echo "//"
#———————————————————————————————————————————————————————————————————————————————————————————————————
randomize()
var dnaSeq = newDnaSeq(200)
echo "Initial sequence"
echo "———————————————\n"
dnaSeq.display()
echo "\nMutations"
echo "—————————\n"
for _ in 1..10:
dnaSeq.mutate()
echo "\nMutated sequence"
echo "————————————————\n"
dnaSeq.display()</syntaxhighlight>
{{out}}
<pre>Initial sequence
———————————————
SQ 200 BP; 53 A; 52 C; 45 G; 50 T; 0 other;
ATGGATAGAA TGGCACCTCA GTGTCACATG TCCTAGGCAC ATTCTACGTA CTAGTTTCTG 60
GAGGTCGATA AATACAAGAT GGAATACTCT TATCAACCGC TAGCAATGAA ACTTAGATAG 120
CCACCCCTCG ATCGCGGTTC GCTATGCGGC ATCGTCAACT GCGTCAAAGC ACTACGTCGT 180
TTCGTGACTG CCAGTCGAGC 200
//
Mutations
—————————
Inserting base A at position 121
Changing base at position 101 from T to G
Deleting base A at position 115
Changing base at position 126 from C to G
Deleting base T at position 155
Deleting base G at position 198
Deleting base T at position 159
Changing base at position 144 from A to T
Inserting base C at position 34
Changing base at position 127 from G to G
Mutated sequence
————————————————
SQ 198 BP; 52 A; 52 C; 46 G; 48 T; 0 other;
ATGGATAGAA TGGCACCTCA GTGTCACATG TCCCTAGGCA CATTCTACGT ACTAGTTTCT 60
GGAGGTCGAT AAATACAAGA TGGAATACTC TTATCAACCG CGAGCAATGA AACTTGATAG 120
ACCACCGCTC GATCGCGGTT CGCTTTGCGG CATCGCAACG CGTCAAAGCA CTACGTCGTT 180
TCGTGACTGC CAGTCGAC 198
//</pre>
=={{header|Perl}}==
{{trans|
<
use warnings;
use feature 'say';
Line 885 ⟶ 2,962:
say "Total bases: ". length $mutate;
say "$_: $cnt{$_}" for @bases;
</syntaxhighlight>
{{out}}
<pre>Original DNA strand:
Line 910 ⟶ 2,987:
G: 51
T: 51</pre>
=={{header|Phix}}==
<!--<syntaxhighlight lang="phix">(phixonline)-->
<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;">200</span><span style="color: #0000FF;">+</span><span style="color: #7060A8;">rand</span><span style="color: #0000FF;">(</span><span style="color: #000000;">300</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: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">dna</span><span style="color: #0000FF;">)</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: #0000FF;">)]</span> <span style="color: #008080;">end</span> <span style="color: #008080;">for</span>
<span style="color: #008080;">procedure</span> <span style="color: #000000;">show</span><span style="color: #0000FF;">()</span>
<span style="color: #004080;">sequence</span> <span style="color: #000000;">acgt</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">repeat</span><span style="color: #0000FF;">(</span><span style="color: #000000;">0</span><span style="color: #0000FF;">,</span><span style="color: #000000;">5</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: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">dna</span><span style="color: #0000FF;">)</span> <span style="color: #008080;">do</span>
<span style="color: #000000;">acgt</span><span style="color: #0000FF;">[</span><span style="color: #7060A8;">find</span><span style="color: #0000FF;">(</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: #008000;">"ACGT"</span><span style="color: #0000FF;">)]</span> <span style="color: #0000FF;">+=</span> <span style="color: #000000;">1</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">for</span>
<span style="color: #000000;">acgt</span><span style="color: #0000FF;">[$]</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">sum</span><span style="color: #0000FF;">(</span><span style="color: #000000;">acgt</span><span style="color: #0000FF;">)</span>
<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: #008000;">"\n"</span><span style="color: #0000FF;">),</span><span style="color: #000000;">1</span><span style="color: #0000FF;">,</span><span style="color: #000000;">5</span><span style="color: #0000FF;">,</span><span style="color: #008000;">" "</span><span style="color: #0000FF;">)),</span><span style="color: #008000;">"\n"</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: #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;">i</span><span style="color: #0000FF;">-</span><span style="color: #000000;">1</span><span style="color: #0000FF;">)*</span><span style="color: #000000;">50</span><span style="color: #0000FF;">+</span><span style="color: #000000;">1</span><span style="color: #0000FF;">,</span><span style="color: #000000;">s</span><span style="color: #0000FF;">[</span><span style="color: #000000;">i</span><span style="color: #0000FF;">]})</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">for</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;">"\nBase counts: A:%d, C:%d, G:%d, T:%d, total:%d\n"</span><span style="color: #0000FF;">,</span><span style="color: #000000;">acgt</span><span style="color: #0000FF;">)</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">procedure</span>
<span style="color: #008080;">procedure</span> <span style="color: #000000;">mutate</span><span style="color: #0000FF;">()</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;">"\n"</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;">10</span> <span style="color: #008080;">do</span>
<span style="color: #004080;">integer</span> <span style="color: #000000;">p</span> <span style="color: #0000FF;">=</span> <span style="color: #7060A8;">rand</span><span style="color: #0000FF;">(</span><span style="color: #7060A8;">length</span><span style="color: #0000FF;">(</span><span style="color: #000000;">dna</span><span style="color: #0000FF;">)),</span>
<span style="color: #000000;">sdi</span> <span style="color: #0000FF;">=</span> <span style="color: #008000;">"SDI"</span><span style="color: #0000FF;">[</span><span style="color: #7060A8;">rand</span><span style="color: #0000FF;">(</span><span style="color: #000000;">3</span><span style="color: #0000FF;">)],</span>
<span style="color: #000000;">rep</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: #0000FF;">)],</span>
<span style="color: #000000;">was</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">dna</span><span style="color: #0000FF;">[</span><span style="color: #000000;">p</span><span style="color: #0000FF;">]</span>
<span style="color: #008080;">switch</span> <span style="color: #000000;">sdi</span> <span style="color: #008080;">do</span>
<span style="color: #008080;">case</span> <span style="color: #008000;">'S'</span><span style="color: #0000FF;">:</span><span style="color: #000000;">dna</span><span style="color: #0000FF;">[</span><span style="color: #000000;">p</span><span style="color: #0000FF;">]</span> <span style="color: #0000FF;">=</span> <span style="color: #000000;">rep</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;">"swapped %c at %d for %c\n"</span><span style="color: #0000FF;">,{</span><span style="color: #000000;">was</span><span style="color: #0000FF;">,</span><span style="color: #000000;">p</span><span style="color: #0000FF;">,</span><span style="color: #000000;">rep</span><span style="color: #0000FF;">})</span>
<span style="color: #008080;">case</span> <span style="color: #008000;">'D'</span><span style="color: #0000FF;">:</span><span style="color: #000000;">dna</span><span style="color: #0000FF;">[</span><span style="color: #000000;">p</span><span style="color: #0000FF;">..</span><span style="color: #000000;">p</span><span style="color: #0000FF;">]</span> <span style="color: #0000FF;">=</span> <span style="color: #008000;">""</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;">"deleted %c at %d\n"</span><span style="color: #0000FF;">,{</span><span style="color: #000000;">was</span><span style="color: #0000FF;">,</span><span style="color: #000000;">p</span><span style="color: #0000FF;">})</span>
<span style="color: #008080;">case</span> <span style="color: #008000;">'I'</span><span style="color: #0000FF;">:</span><span style="color: #000000;">dna</span><span style="color: #0000FF;">[</span><span style="color: #000000;">p</span><span style="color: #0000FF;">..</span><span style="color: #000000;">p</span><span style="color: #0000FF;">-</span><span style="color: #000000;">1</span><span style="color: #0000FF;">]</span> <span style="color: #0000FF;">=</span> <span style="color: #008000;">""</span><span style="color: #0000FF;">&</span><span style="color: #000000;">rep</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;">"inserted %c at %d, before %c\n"</span><span style="color: #0000FF;">,{</span><span style="color: #000000;">rep</span><span style="color: #0000FF;">,</span><span style="color: #000000;">p</span><span style="color: #0000FF;">,</span><span style="color: #000000;">was</span><span style="color: #0000FF;">})</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">switch</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">for</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;">"\n"</span><span style="color: #0000FF;">)</span>
<span style="color: #008080;">end</span> <span style="color: #008080;">procedure</span>
<span style="color: #000000;">show</span><span style="color: #0000FF;">()</span>
<span style="color: #000000;">mutate</span><span style="color: #0000FF;">()</span>
<span style="color: #000000;">show</span><span style="color: #0000FF;">()</span>
<!--</syntaxhighlight>-->
{{out}}
<pre>
Line 986 ⟶ 3,064:
Base counts: A:128, C:110, G:119, T:123, total:480
</pre>
=={{header|PureBasic}}==
<syntaxhighlight lang="purebasic">#BASE$="ACGT"
#SEQLEN=200
#PROTOCOL=#True
Global dna.s
Define i.i
Procedure pprint()
Define p.i, cnt.i, sum.i
For p=1 To Len(dna) Step 50
Print(RSet(Str(p-1)+": ",5))
PrintN(Mid(dna,p,50))
Next
PrintN("Base counts:")
For p=1 To 4
cnt=CountString(dna,Mid(#BASE$,p,1)) : sum+cnt
Print(Mid(#BASE$,p,1)+": "+Str(cnt)+", ")
Next
PrintN("Total: "+Str(sum))
EndProcedure
Procedure InsertAtPos(basenr.i,position.i)
If #PROTOCOL : PrintN("Insert base "+Mid(#BASE$,basenr,1)+" at position "+Str(position)) : EndIf
dna=InsertString(dna,Mid(#BASE$,basenr,1),position)
EndProcedure
Procedure EraseAtPos(position.i)
If #PROTOCOL : PrintN("Erase base "+Mid(dna,position,1)+" at position "+Str(position)) : EndIf
If position>0 And position<=Len(dna)
dna=Left(dna,position-1)+Right(dna,Len(dna)-position)
EndIf
EndProcedure
Procedure OverwriteAtPos(basenr.i,position.i)
If #PROTOCOL : PrintN("Change base at position "+Str(position)+" from "+Mid(dna,position,1)+" to "+Mid(#BASE$,basenr,1)) : EndIf
If position>0 And position<=Len(dna)
position-1
PokeS(@dna+2*position,Mid(#BASE$,basenr,1),-1,#PB_String_NoZero)
EndIf
EndProcedure
If OpenConsole()=0 : End 1 : EndIf
For i=1 To #SEQLEN : dna+Mid(#BASE$,Random(4,1),1) : Next
PrintN("Initial sequence:")
pprint()
For i=1 To 10
Select Random(2)
Case 0 : InsertAtPos(Random(4,1),Random(Len(dna),1))
Case 1 : EraseAtPos(Random(Len(dna),1))
Case 2 : OverwriteAtPos(Random(4,1),Random(Len(dna),1))
EndSelect
Next
PrintN("After 10 mutations:")
pprint()
Input()</syntaxhighlight>
{{out}}
<pre>Initial sequence:
0: AAGTTTACGTCGGACTTCATTAATCGGTTTAGTCAGACCCGATCCAAATC
50: TTGCTTTCACTCCGCATTCTTCTCATGAGTAAAAGGCTGCTCCTGCACTA
100: AAGCGTTCTCAACACCTTGGAGAGCCATCTCGGTACTCCGCGCAAAATAG
150: CCATAGAGGGTATCAGGAAACGCATCGAAGGTTTAGCCGAACTAAGGTCT
Base counts:
A: 54, C: 52, G: 42, T: 52, Total: 200
Change base at position 7 from A to T
Insert base T at position 66
Erase base G at position 198
Insert base C at position 32
Change base at position 80 from A to G
Erase base A at position 2
Insert base C at position 33
Insert base C at position 201
Insert base G at position 70
Erase base T at position 187
After 10 mutations:
0: AGTTTTCGTCGGACTTCATTAATCGGTTTACGCTCAGACCCGATCCAAAT
50: CTTGCTTTCACTCCGCTATGTCTTCTCATGGGTAAAAGGCTGCTCCTGCA
100: CTAAAGCGTTCTCAACACCTTGGAGAGCCATCTCGGTACTCCGCGCAAAA
150: TAGCCATAGAGGGTATCAGGAAACGCATCGAAGGTTAGCCGAACTAAGTC
200: CT
Base counts:
A: 51, C: 55, G: 43, T: 53, Total: 202</pre>
=={{header|Python}}==
In function seq_mutate argument kinds selects between the three kinds of mutation. The characters I, D, and S are chosen from the string to give the kind of mutation to perform, so the more of that character, the more of that type of mutation performed.<br>
Similarly parameter choice is chosen from to give the base for substitution or insertion - the more any base appears, the more likely it is to be chosen in any insertion/substitution.
<
from collections import Counter
Line 1,036 ⟶ 3,198:
print(f" {kind:>10} @{index}")
print()
seq_pp(mseq)</
{{out}}
Line 1,079 ⟶ 3,241:
T: 72
TOT= 251</pre>
=={{header|Quackery}}==
<code>prettyprint</code> and <code>tallybases</code> are defined at [[Bioinformatics/base count#Quackery]].
<syntaxhighlight lang="quackery"> [ $ "ACGT" 4 random peek ] is randomgene ( --> c )
[ $ "" swap times
[ randomgene join ] ] is randomsequence ( n --> $ )
[ dup size random
3 random
[ table
[ pluck drop ]
[ randomgene unrot stuff ]
[ randomgene unrot poke ] ]
do ] is mutate ( $ --> $ )
200 randomsequence
dup prettyprint cr cr dup tallybases
cr cr say "Mutating..." cr
10 times mutate
dup prettyprint cr cr tallybases</syntaxhighlight>
{{out}}
<pre> 0 CGCCCGCACC TAGAACCATT AAGCTGTCTG GTGTCGGGAT CGTCACATTA
50 CGCCCCTTGT TGCGTCGGCG CCGATGCGAA GGCATAATAT GTGGTCTAAT
100 GTCATGCGTG CCCGGGGAAT CTGGCGCGAC CGTCATGGCA AACCGCATCC
150 CCTCAGCAAA TTACTAGCTG GTTGATTTTC ATCATAGGCC TGATCATGTG
adenine 41
cytosine 56
guanine 53
thymine 50
total 200
Mutating...
0 AGGCCCGCAC CTAGAACCAT TAAGCTGTCT GGTGTCGGGA TCGTCACATT
50 ACGCCCCTTG TGCGTCGGCG CCGATGCGAA GGCATAATAT GTGGTCTGAT
100 GTCATGCGTG CGCGGGGAAT CTGGCGCGAC CGTCATGGCA AACCGCATCC
150 CCTCAGCAAA ATTCTAGCTG GTTGATTTTA TCTATAGGCC TGACTCATGT
200 G
adenine 41
cytosine 54
guanine 56
thymine 50
total 201
</pre>
=={{header|Racket}}==
<syntaxhighlight lang="racket">#lang racket
(define current-S-weight (make-parameter 1))
(define current-D-weight (make-parameter 1))
(define current-I-weight (make-parameter 1))
(define bases '(#\A #\C #\G #\T))
(define (fold-sequence seq kons #:finalise (finalise (λ x (apply values x))) . k0s)
(define (recur seq . ks)
(if (null? seq)
(call-with-values (λ () (apply finalise ks)) (λ vs (apply values vs)))
(call-with-values (λ () (apply kons (car seq) ks)) (λ ks+ (apply recur (cdr seq) ks+)))))
(apply recur (if (string? seq) (string->list (regexp-replace* #px"[^ACGT]" seq "")) seq) k0s))
(define (sequence->pretty-printed-string seq)
(define (fmt idx cs-rev) (format "~a: ~a" (~a idx #:width 3 #:align 'right) (list->string (reverse cs-rev))))
(fold-sequence
seq
(λ (b n start-idx lns-rev cs-rev)
(if (zero? (modulo n 50))
(values (+ n 1) n (if (pair? cs-rev) (cons (fmt start-idx cs-rev) lns-rev) lns-rev) (cons b null))
(values (+ n 1) start-idx lns-rev (cons b cs-rev))))
0 0 null null
#:finalise (λ (n idx lns-rev cs-rev)
(string-join (reverse (if (null? cs-rev) lns-rev (cons (fmt idx cs-rev) lns-rev))) "\n"))))
(define (count-bases b as cs gs ts n)
(values (+ as (if (eq? b #\A) 1 0)) (+ cs (if (eq? b #\C) 1 0)) (+ gs (if (eq? b #\T) 1 0)) (+ ts (if (eq? b #\G) 1 0)) (add1 n)))
(define (report-sequence s)
(define-values (as cs gs ts n) (fold-sequence s count-bases 0 0 0 0 0))
(printf "SEQUENCE:~%~a~%" (sequence->pretty-printed-string s))
(printf "BASE COUNT:~%-----------~%~a~%"
(string-join (map (λ (c n) (format " ~a :~a" c (~a #:width 4 #:align 'right n))) bases (list as ts cs gs)) "\n"))
(printf "TOTAL: ~a~%" n))
(define (make-random-sequence-string l)
(list->string (for/list ((_ l)) (list-ref bases (random 4)))))
(define (weighted-random-call weights-and-functions . args)
(let loop ((r (random)) (wfs weights-and-functions))
(if (<= r (car wfs)) (apply (cadr wfs) args) (loop (- r (car wfs)) (cddr wfs)))))
(define (mutate-S s)
(let ((r (random (string-length s))) (i (string (list-ref bases (random 4)))))
(printf "Mutate at ~a -> ~a~%" r i)
(string-append (substring s 0 r) i (substring s (add1 r)))))
(define (mutate-D s)
(let ((r (random (string-length s))))
(printf "Delete at ~a~%" r)
(string-append (substring s 0 r) (substring s (add1 r)))))
(define (mutate-I s)
(let ((r (random (string-length s))) (i (string (list-ref bases (random 4)))))
(printf "Insert at ~a -> ~a~%" r i)
(string-append (substring s 0 r) i (substring s r))))
(define (mutate s)
(define W (+ (current-S-weight) (current-D-weight) (current-I-weight)))
(weighted-random-call
(list (/ (current-S-weight) W) mutate-S (/ (current-D-weight) W) mutate-D (/ (current-I-weight) W) mutate-I)
s))
(module+
main
(define initial-sequence (make-random-sequence-string 200))
(report-sequence initial-sequence)
(newline)
(define s+ (for/fold ((s initial-sequence)) ((_ 10)) (mutate s)))
(newline)
(report-sequence s+)
(newline)
(define s+d (parameterize ((current-D-weight 5)) (for/fold ((s initial-sequence)) ((_ 10)) (mutate s))))
(newline)
(report-sequence s+d))</syntaxhighlight>
{{out}}
<pre>SEQUENCE:
0: AATGCTTGTGTCACCGGCCACCCCCTATGTACATACACGGTTCAGCTGGC
50: CTGGCAGAGCGTCTGACAACGGAGCTCTAAAACTTCCTTCTGACTAGAGC
100: TCATCCTCTCCCGGCTGAACTCCGTGGCTTACAATCAGACCCTACCCGTG
150: TCCAACTACGCAGTCGCCCGATGAGGCTGGGCTCACCACGTTGGGCGAGG
BASE COUNT:
-----------
A : 41
C : 49
G : 67
T : 43
TOTAL: 200
Insert at 176 -> T
Insert at 99 -> G
Delete at 154
Mutate at 188 -> A
Insert at 14 -> A
Mutate at 62 -> G
Delete at 110
Mutate at 79 -> T
Insert at 109 -> A
Insert at 46 -> C
SEQUENCE:
0: AATGCTTGTGTCACACGGCCACCCCCTATGTACATACACGGTTCAGCCTG
50: GCCTGGCAGAGCGGCTGACAACGGAGCTCTTAAACTTCCTTCTGACTAGA
100: GGCTCATCCTACCCCGGCTGAACTCCGTGGCTTACAATCAGACCCTACCC
150: GTGTCCACTACGCAGTCGCCCGATGAGGTCTGGGCTCACCACGTTGGGCG
200: AGG
BASE COUNT:
-----------
A : 41
C : 51
G : 68
T : 43
TOTAL: 203
Delete at 79
Delete at 105
Delete at 63
Delete at 37
Delete at 166
Mutate at 42 -> C
Delete at 142
Delete at 23
Delete at 91
Insert at 4 -> T
SEQUENCE:
0: AATGTCTTGTGTCACCGGCCACCCCTATGTACATACAGGTTCCGCTGGCC
50: TGGCAGAGCGTCGACAACGGAGCTCTAAACTTCCTTCTGACTGAGCTCAT
100: CCCTCCCGGCTGAACTCCGTGGCTTACAATCAGACCCTACCGTGTCCAAC
150: TACGCAGTCGCCCGTGAGGCTGGGCTCACCACGTTGGGCGAGG
BASE COUNT:
-----------
A : 37
C : 49
G : 65
T : 42
TOTAL: 193</pre>
=={{header|Raku}}==
(formerly Perl 6)
Line 1,086 ⟶ 3,442:
<syntaxhighlight lang="raku"
# The DNA strand
Line 1,117 ⟶ 3,473:
sub diff ($orig, $repl) {
($orig.comb Z $repl.comb).map( -> ($o, $r) { $o eq $r ?? $o !! $r.lc }).join
}</
{{out}}
<pre>ORIGINAL DNA STRAND:
Line 1,142 ⟶ 3,498:
G 43
T 53</pre>
=={{header|Ring}}==
<syntaxhighlight lang="ring">
row = 0
dnaList = []
base = ["A","C","G","T"]
long = 20
see "Initial sequence:" + nl
see " 12345678901234567890" + 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
see nl+ " 12345678901234567890" + nl
baseCount(dnaList)
for n = 1 to 10
rnd = random(2)+1
switch rnd
on 1
baseSwap(dnaList)
on 2
baseDelete(dnaList)
on 3
baseInsert(dnaList)
off
next
showDna(dnaList)
baseCount(dnaList)
func baseInsert(dnaList)
rnd1 = random(len(dnaList)-1)+1
rnd2 = random(len(base)-1)+1
insert(dnaList,rnd1,base[rnd2])
see "Insert base " + base[rnd2] + " at position " + rnd1 + nl
return dnaList
func baseDelete(dnaList)
rnd = random(len(dnaList)-1)+1
del(dnaList,rnd)
see "Erase base " + dnaList[rnd] + " at position " + rnd + nl
return dnaList
func baseSwap(dnaList)
rnd1 = random(len(dnaList))
rnd2 = random(3)+1
see "Change base at position " + rnd1 + " from " + dnaList[rnd1] + " to " + base[rnd2] + nl
dnaList[rnd1] = base[rnd2]
func showDna(dnaList)
long = 20
see nl + "After 10 mutations:" + nl
see " 12345678901234567890" + nl
see " " + long + ": "
for nr = 1 to len(dnaList)
row = row + 1
see dnaList[nr]
if (row%20) = 0 and long < 200
long = long + 20
see nl
if long < 100
see " " + long + ": "
else
see "" + long + ": "
ok
ok
next
see nl+ " 12345678901234567890" + nl
func baseCount(dnaList)
dnaBase = [:A=0, :C=0, :G=0, :T=0]
lenDna = len(dnaList)
for n = 1 to lenDna
dnaStr = dnaList[n]
switch dnaStr
on "A"
strA = dnaBase["A"]
strA++
dnaBase["A"] = strA
on "C"
strC = dnaBase["C"]
strC++
dnaBase["C"] = strC
on "G"
strG = dnaBase["G"]
strG++
dnaBase["G"] = strG
on "T"
strT = dnaBase["T"]
strT++
dnaBase["T"] = strT
off
next
see nl
see "A: " + dnaBase["A"] + ", "
see "T: " + dnaBase["T"] + ", "
see "C: " + dnaBase["C"] + ", "
see "G: " + dnaBase["G"] + ", "
total = dnaBase["A"] + dnaBase["T"] + dnaBase["C"] + dnaBase["G"]
see "Total: " + total+ nl + nl
</syntaxhighlight>
{{out}}
<pre>
Initial sequence:
12345678901234567890
20: GGAGACACTAACGAAACAAA
40: CAGGTATATAGGACATGTAG
60: AAACAATTAATACGTAGCGA
80: ACTGTGGCGCGAAAGAAGGG
100: ATGGACTCGGGTATTGCCGA
120: GATTCACGCCAACGAAAAAT
140: ATCTCAGATGACCGAAATAG
160: GGTCATCGAAATGAGTCCAA
180: ATAACTAAGTGGACAAAGGT
200: AGACCAAAAAGGACAGAAAA
12345678901234567890
A: 84, T: 32, C: 34, G: 50, Total: 200
Change base at position 176 from A to A
Change base at position 178 from G to C
Change base at position 180 from T to C
Erase base T at position 28
Insert base A at position 17
Erase base C at position 52
Change base at position 118 from A to A
Insert base T at position 192
Insert base A at position 142
Erase base A at position 18
After 10 mutations:
12345678901234567890
20: GGAGACACTAACGAAACAAA
40: CAGGTATTAGGACATGTAGA
60: AACAATTAATCGTAGCGAAC
80: TGTGGCGCGAAAGAAGGGAT
100: GGACTCGGGTATTGCCGAGA
120: TTCACGCCAACGAAAAATAT
140: CTCAGATGACCGAAATAGGG
160: TACATCGAAATGAGTCCAAA
180: TAACTAAGTGGACAAACGCA
200: GACCAAAAAGGATCAGAAAA
12345678901234567890
A: 83, T: 32, C: 36, G: 49, Total: 200
</pre>
=={{header|Ruby}}==
<syntaxhighlight lang="ruby">class DNA_Seq
attr_accessor :seq
def initialize(bases: %i[A C G T] , size: 0)
@bases = bases
@seq = Array.new(size){ bases.sample }
end
def mutate(n = 10)
n.times{|n| method([:s, :d, :i].sample).call}
end
def to_s(n = 50)
just_size = @seq.size / n
(0...@seq.size).step(n).map{|from| "#{from.to_s.rjust(just_size)} " + @seq[from, n].join}.join("\n") +
"\nTotal #{seq.size}: #{@seq.tally.sort.to_h.inspect}\n\n"
end
def s = @seq[rand_index]= @bases.sample
def d = @seq.delete_at(rand_index)
def i = @seq.insert(rand_index, @bases.sample )
alias :swap :s
alias :delete :d
alias :insert :i
private
def rand_index = rand( @seq.size )
end
puts test = DNA_Seq.new(size: 200)
test.mutate
puts test
test.delete
puts test
</syntaxhighlight>
{{out}}
<pre> 0 TAAGGTGAGGAGTGTGATGGAGTTCGGTGGCTAGCCACAAATACAACACA
50 CTCACCCATACTCGCCTCTGAAGCATGTTTTACTTGGATAGGGCCTACAG
100 CAGTATTCACCCATTCCTCGGCTCCTGACCTGATGTAGGTCTATGTGCGG
150 GAAAATAGGACAATACTGCCGAAGTCATATCCATTGGAGGGGCCCCAGGC
Total 200: {:A=>51, :C=>50, :G=>52, :T=>47}
0 TAAGCTGAGGTGTGTGATGGAGTTCGGTGGCTAGCCACAAATACAACACA
50 CTCACCCATACTCGCCTCTGAAGCATGTTTTAATTGGATAGGGCCTACAG
100 CAGTATTCACCCTTCCTCCGCTCCTGACCTGATATAGGTCTATGTGCGGG
150 AAAATAGGACAATACTGCCGAAGTCATATCCATTGGAGGGGCCCCAAGGC
Total 200: {:A=>52, :C=>51, :G=>49, :T=>48}
0 TAAGCTGAGGTGTGTGATGGAGTTCGGTGGCTAGCCACAAATACAACACA
50 CTCACCCATACTCGCTCTGAAGCATGTTTTAATTGGATAGGGCCTACAGC
100 AGTATTCACCCTTCCTCCGCTCCTGACCTGATATAGGTCTATGTGCGGGA
150 AAATAGGACAATACTGCCGAAGTCATATCCATTGGAGGGGCCCCAAGGC
Total 199: {:A=>52, :C=>50, :G=>49, :T=>48}
</pre>
=={{header|Rust}}==
<syntaxhighlight lang="rust">
use rand::prelude::*;
use std::collections::HashMap;
use std::fmt::{Display, Formatter, Error};
pub struct Seq<'a> {
alphabet: Vec<&'a str>,
distr: rand::distributions::Uniform<usize>,
pos_distr: rand::distributions::Uniform<usize>,
seq: Vec<&'a str>,
}
impl Display for Seq<'_> {
fn fmt(&self, f: &mut Formatter) -> Result<(), Error> {
let pretty: String = self.seq
.iter()
.enumerate()
.map(|(i, nt)| if (i + 1) % 60 == 0 { format!("{}\n", nt) } else { nt.to_string() })
.collect();
let counts_hm = self.seq
.iter()
.fold(HashMap::<&str, usize>::new(), |mut m, nt| {
*m.entry(nt).or_default() += 1;
m
});
let mut counts_vec: Vec<(&str, usize)> = counts_hm.into_iter().collect();
counts_vec.sort_by(|a, b| a.0.cmp(&b.0));
let counts_string = counts_vec
.iter()
.fold(String::new(), |mut counts_string, (nt, count)| {
counts_string += &format!("{} = {}\n", nt, count);
counts_string
});
write!(f, "Seq:\n{}\n\nLength: {}\n\nCounts:\n{}", pretty, self.seq.len(), counts_string)
}
}
impl Seq<'_> {
pub fn new(alphabet: Vec<&str>, len: usize) -> Seq {
let distr = rand::distributions::Uniform::new_inclusive(0, alphabet.len() - 1);
let pos_distr = rand::distributions::Uniform::new_inclusive(0, len - 1);
let seq: Vec<&str> = (0..len)
.map(|_| {
alphabet[thread_rng().sample(distr)]
})
.collect();
Seq { alphabet, distr, pos_distr, seq }
}
pub fn insert(&mut self) {
let pos = thread_rng().sample(self.pos_distr);
let nt = self.alphabet[thread_rng().sample(self.distr)];
println!("Inserting {} at position {}", nt, pos);
self.seq.insert(pos, nt);
}
pub fn delete(&mut self) {
let pos = thread_rng().sample(self.pos_distr);
println!("Deleting {} at position {}", self.seq[pos], pos);
self.seq.remove(pos);
}
pub fn swap(&mut self) {
let pos = thread_rng().sample(self.pos_distr);
let cur_nt = self.seq[pos];
let new_nt = self.alphabet[thread_rng().sample(self.distr)];
println!("Replacing {} at position {} with {}", cur_nt, pos, new_nt);
self.seq[pos] = new_nt;
}
}
fn main() {
let mut seq = Seq::new(vec!["A", "C", "T", "G"], 200);
println!("Initial sequnce:\n{}", seq);
let mut_distr = rand::distributions::Uniform::new_inclusive(0, 2);
for _ in 0..10 {
let mutation = thread_rng().sample(mut_distr);
if mutation == 0 {
seq.insert()
} else if mutation == 1 {
seq.delete()
} else {
seq.swap()
}
}
println!("\nMutated sequence:\n{}", seq);
}
</syntaxhighlight>
{{out}}
<pre>
Initial sequnce:
Seq:
TAAGTTTAGTCTGTTTACGAGATCTAGAGGAGGACACCGTGTAGAGGGGATTTGTCAGGA
CACATGCATGGCACCCTAGTCAAATAGTGCCGAGAACAGGCTCTCCTGAGAAAGTTAGGT
CTGCCGAAGTGACGAAGTGCACGTTATAGCTCTATTAAGTATGTTCGTTAACAGGTATTA
ATGCTCTTAGCCAAGACCGT
Length: 200
Counts:
A = 56
C = 38
G = 53
T = 53
Deleting C at position 197
Inserting T at position 157
Replacing C at position 149 with G
Replacing A at position 171 with G
Replacing T at position 182 with G
Deleting C at position 124
Inserting T at position 128
Replacing G at position 175 with C
Deleting A at position 35
Replacing A at position 193 with G
Mutated sequence:
Seq:
TAAGTTTAGTCTGTTTACGAGATCTAGAGGAGGACCCGTGTAGAGGGGATTTGTCAGGAC
ACATGCATGGCACCCTAGTCAAATAGTGCCGAGAACAGGCTCTCCTGAGAAAGTTAGGTC
TGCGAAGTTGACGAAGTGCACGTTATAGGTCTATTATAGTATGTTCGTTAGCAGCTATTA
AGGCTCTTAGCCAGGACGT
Length: 199
Counts:
A = 53
C = 36
G = 56
T = 54</pre>
=={{header|Swift}}==
<
enum Action: CaseIterable {
Line 1,201 ⟶ 3,912:
}
printSeq(d)</
{{out}}
Line 1,229 ⟶ 3,940:
G: 56
T: 45</pre>
=={{header|V (Vlang)}}==
{{trans|Go}}
<syntaxhighlight lang="v (vlang)">import rand
import rand.seed
const bases = "ACGT"
// 'w' contains the weights out of 300 for each
// of swap, delete or insert in that order.
fn mutate(dna string, w [3]int) string {
le := dna.len
// get a random position in the dna to mutate
p := rand.intn(le) or {0}
// get a random number between 0 and 299 inclusive
r := rand.intn(300) or {0}
mut bytes := dna.bytes()
match true {
r < w[0] { // swap
base := bases[rand.intn(4) or {0}]
println(" Change @${p:3} ${[bytes[p]].bytestr()} to ${[base].bytestr()}")
bytes[p] = base
}
r < w[0]+w[1] { // delete
println(" Delete @${p:3} ${bytes[p]}")
bytes.delete(p)
//copy(bytes[p:], bytes[p+1:])
bytes = bytes[0..le-1]
}
else { // insert
base := bases[rand.intn(4) or {0}]
bytes << 0
bytes.insert(p,bytes[p])
//copy(bytes[p+1:], bytes[p:])
println(" Insert @${p:3} $base")
bytes[p] = base
}
}
return bytes.bytestr()
}
// Generate a random dna sequence of given length.
fn generate(le int) string {
mut bytes := []u8{len:le}
for i := 0; i < le; i++ {
bytes[i] = bases[rand.intn(4) or {0}]
}
return bytes.bytestr()
}
// Pretty print dna and stats.
fn pretty_print(dna string, rowLen int) {
println("SEQUENCE:")
le := dna.len
for i := 0; i < le; i += rowLen {
mut k := i + rowLen
if k > le {
k = le
}
println("${i:5}: ${dna[i..k]}")
}
mut base_map := map[byte]int{} // allows for 'any' base
for i in 0..le {
base_map[dna[i]]++
}
mut bb := base_map.keys()
bb.sort()
println("\nBASE COUNT:")
for base in bb {
println(" $base: ${base_map[base]:3}")
}
println(" ------")
println(" Σ: $le")
println(" ======\n")
}
// Express weights as a string.
fn wstring(w [3]int) string {
return " Change: ${w[0]}\n Delete: ${w[1]}\n Insert: ${w[2]}\n"
}
fn main() {
rand.seed(seed.time_seed_array(2))
mut dna := generate(250)
pretty_print(dna, 50)
muts := 10
w := [100, 100, 100]! // use e.g. {0, 300, 0} to choose only deletions
println("WEIGHTS (ex 300):\n${wstring(w)}")
println("MUTATIONS ($muts):")
for _ in 0..muts {
dna = mutate(dna, w)
}
println('')
pretty_print(dna, 50)
}</syntaxhighlight>
{{out}}
Sample run:
<pre>
SEQUENCE:
0: CATTGGATTGCTAGTCGTTCAATAGCGAACGAACAGTTTGCATGAATCAG
50: AGAGAGCCTGAAACCTTGGTTGGTATCGACACAACCTCATAATTCACATT
100: CACAAACTTATTTTCGGATCCGCGAAAACGCAAGCGCATTAAGAGACACC
150: CCCAGAGACTCAATTCCGGATTTGCGCTGCTATATACCCACATTGATGAT
200: ATAGGGCTTAGAACGGCCTTAGCCCCGTCGGCTAGTTTCTGAAGTCTCTT
BASE COUNT:
A: 71
C: 62
G: 52
T: 65
------
Σ: 250
======
WEIGHTS (ex 300):
Change: 100
Delete: 100
Insert: 100
MUTATIONS (10):
Delete @166 "C"
Change @185 "C" to "G"
Insert @230 "T"
Insert @230 "G"
Insert @226 "C"
Change @162 "A" to "C"
Change @236 "G" to "C"
Insert @ 25 "C"
Delete @ 75 "A"
Change @104 "A" to "T"
SEQUENCE:
0: CATTGGATTGCTAGTCGTTCAATAGCCGAACGAACAGTTTGCATGAATCA
50: GAGAGAGCCTGAAACCTTGGTTGGTTCGACACAACCTCATAATTCACATT
100: CACATACTTATTTTCGGATCCGCGAAAACGCAAGCGCATTAAGAGACACC
150: CCCAGAGACTCACTTCGGATTTGCGCTGCTATATAGCCACATTGATGATA
200: TAGGGCTTAGAACGGCCTTAGCCCCGCTCGGGTCTACTTTCTGAAGTCTC
250: TT
BASE COUNT:
A: 68
C: 64
G: 53
T: 67
------
Σ: 252
======
</pre>
=={{header|Wren}}==
{{trans|Go}}
{{libheader|Wren-sort}}
{{libheader|Wren-fmt}}
<syntaxhighlight lang="wren">import "random" for Random
import "./fmt" for Fmt
import "./sort" for Sort
var rand = Random.new()
var bases = "ACGT"
// 'w' contains the weights out of 300 for each
// of swap, delete or insert in that order.
var mutate = Fn.new { |dna, w|
var le = dna.count
// get a random position in the dna to mutate
var p = rand.int(le)
// get a random number between 0 and 299 inclusive
var r = rand.int(300)
var chars = dna.toList
if (r < w[0]) { // swap
var base = bases[rand.int(4)]
Fmt.print(" Change @$3d $q to $q", p, chars[p], base)
chars[p] = base
} else if (r < w[0] + w[1]) { // delete
Fmt.print(" Delete @$3d $q", p, chars[p])
chars.removeAt(p)
} else { // insert
var base = bases[rand.int(4)]
Fmt.print(" Insert @$3d $q", p, base)
chars.insert(p, base)
}
return chars.join()
}
// Generate a random dna sequence of given length.
var generate = Fn.new { |le|
var chars = [""] * le
for (i in 0...le) chars[i] = bases[rand.int(4)]
return chars.join()
}
// Pretty print dna and stats.
var prettyPrint = Fn.new { |dna, rowLen|
System.print("SEQUENCE:")
var le = dna.count
var i = 0
while (i < le) {
var k = i + rowLen
if (k > le) k = le
Fmt.print("$5d: $s", i, dna[i...k])
i = i + rowLen
}
var baseMap = {}
for (i in 0...le) {
var v = baseMap[dna[i]]
baseMap[dna[i]] = (v) ? v + 1 : 1
}
var bases = []
for (k in baseMap.keys) bases.add(k)
Sort.insertion(bases) // get bases into alphabetic order
System.print("\nBASE COUNT:")
for (base in bases) Fmt.print(" $s: $3d", base, baseMap[base])
System.print(" ------")
System.print(" Σ: %(le)")
System.print(" ======\n")
}
// Express weights as a string.
var wstring = Fn.new { |w|
return Fmt.swrite(" Change: $d\n Delete: $d\n Insert: $d\n", w[0], w[1], w[2])
}
var dna = generate.call(250)
prettyPrint.call(dna, 50)
var muts = 10
var w = [100, 100, 100] // use e.g. {0, 300, 0} to choose only deletions
Fmt.print("WEIGHTS (ex 300):\n$s", wstring.call(w))
Fmt.print("MUTATIONS ($d):", muts)
for (i in 0...muts) dna = mutate.call(dna, w)
System.print()
prettyPrint.call(dna, 50)</syntaxhighlight>
{{out}}
Sample run:
<pre>
SEQUENCE:
0: CATTGGATTGCTAGTCGTTCAATAGCGAACGAACAGTTTGCATGAATCAG
50: AGAGAGCCTGAAACCTTGGTTGGTATCGACACAACCTCATAATTCACATT
100: CACAAACTTATTTTCGGATCCGCGAAAACGCAAGCGCATTAAGAGACACC
150: CCCAGAGACTCAATTCCGGATTTGCGCTGCTATATACCCACATTGATGAT
200: ATAGGGCTTAGAACGGCCTTAGCCCCGTCGGCTAGTTTCTGAAGTCTCTT
BASE COUNT:
A: 71
C: 62
G: 52
T: 65
------
Σ: 250
======
WEIGHTS (ex 300):
Change: 100
Delete: 100
Insert: 100
MUTATIONS (10):
Delete @166 "C"
Change @185 "C" to "G"
Insert @230 "T"
Insert @230 "G"
Insert @226 "C"
Change @162 "A" to "C"
Change @236 "G" to "C"
Insert @ 25 "C"
Delete @ 75 "A"
Change @104 "A" to "T"
SEQUENCE:
0: CATTGGATTGCTAGTCGTTCAATAGCCGAACGAACAGTTTGCATGAATCA
50: GAGAGAGCCTGAAACCTTGGTTGGTTCGACACAACCTCATAATTCACATT
100: CACATACTTATTTTCGGATCCGCGAAAACGCAAGCGCATTAAGAGACACC
150: CCCAGAGACTCACTTCGGATTTGCGCTGCTATATAGCCACATTGATGATA
200: TAGGGCTTAGAACGGCCTTAGCCCCGCTCGGGTCTACTTTCTGAAGTCTC
250: TT
BASE COUNT:
A: 68
C: 64
G: 53
T: 67
------
Σ: 252
======
</pre>
=={{header|Yabasic}}==
{{trans|Phix}}
<syntaxhighlight lang="yabasic">// Rosetta Code problem: http://rosettacode.org/wiki/Sequence_mutation
// by Galileo, 07/2022
r = int(ran(300))
for i = 1 to 200 + r : dna$ = dna$ + mid$("ACGT", int(ran(4))+1, 1) : next
sub show()
local acgt(4), i, j, x, total
for i = 1 to len(dna$)
x = instr("ACGT", mid$(dna$, i, 1))
acgt(x) = acgt(x) + 1
next
for i = 1 to 4 : total = total + acgt(i) : next
for i = 1 to len(dna$) step 50
print i, ":\t";
for j = 0 to 49 step 10
print mid$(dna$, i+j, 10), " ";
next
print
next
print "\nBase counts: A: ", acgt(1), ", C: ", acgt(2), ", G: ", acgt(3), ", T: ", acgt(4), ", total: ", total
end sub
sub mutate()
local i, p, sdi$, rep$, was$
print
for i = 1 to 10
p = int(ran(len(dna$))) + 1
sdi$ = mid$("SDI", int(ran(3)) + 1, 1)
rep$ = mid$("ACGT", int(ran(4)) + 1, 1)
was$ = mid$(dna$, p, 1)
switch sdi$
case "S": mid$(dna$, p, 1) = rep$
print "swapped ", was$, " at ", p, " for ", rep$ : break
case "D": dna$ = left$(dna$, p - 1) + right$(dna$, len(dna$) - p)
print "deleted ", was$, " at ", p : break
case "I": dna$ = left$(dna$, p - 1) + rep$ + right$(dna$, (len(dna$) - p + 1))
print "inserted ", rep$, " at ", p, ", before ", was$ : break
end switch
next
print
end sub
show()
mutate()
show()</syntaxhighlight>
{{out}}
<pre>1: TCCATCGTGG GATCGCTCTA GCGGTATGCT ATCATTCCTA TAGCAATTCT
51: CAGGGGGCCC GACGGCGCCG ATCACATGTG ATCCTTGTGT GATCGCTTCA
101: TGTCATGGCT TTCTAGACCT TGGATAAGCA TGTACGGTTG GACCAGTCGT
151: GCGTCGGTAA ACAACGCATC TGTGTTATAT CCGTCGAATA ACCCATATGT
201: CTCCAGTCTA ATCCCCTAAG CAACTGCTCA AGGTAAAATG CAAATACAGG
251: TGAGGAGTCC TCGAAGGGGT CGCACCGCAA TATGGGCGTC CCTTATTGGC
301: CCTCATCAGT AT
Base counts: A: 72, C: 81, G: 76, T: 83, total: 312
inserted G at 89, before G
swapped T at 174 for C
deleted A at 31
deleted G at 89
deleted C at 275
inserted A at 278, before A
inserted C at 200, before C
inserted C at 232, before G
deleted G at 10
swapped A at 124 for C
1: TCCATCGTGG ATCGCTCTAG CGGTATGCTT CATTCCTATA GCAATTCTCA
51: GGGGGCCCGA CGGCGCCGAT CACATGTGAT CCTTGTGTGA TCGCTTCATG
101: TCATGGCTTT CTAGACCTTG GATCAGCATG TACGGTTGGA CCAGTCGTGC
151: GTCGGTAAAC AACGCATCTG CGTTATATCC GTCGAATAAC CCATATGTCC
201: TCCAGTCTAA TCCCCTAAGC AACTGCTCAA CGGTAAAATG CAAATACAGG
251: TGAGGAGTCC TCGAAGGGGT CGCACGCAAA TATGGGCGTC CCTTATTGGC
301: CCTCATCAGT AT
Base counts: A: 71, C: 84, G: 75, T: 82, total: 312
---Program done, press RETURN---</pre>
=={{header|zkl}}==
<
dna:=(190).pump(Data().howza(3),(0).random.fp(0,4),bases.get); // bucket of bytes
Line 1,263 ⟶ 4,347:
[0..*,50].zipWith(fcn(n,bases){ println("%6d: %s".fmt(n,bases.concat())) },
dna.walker().walk.fp(50)).pump(Void); // .pump forces the iterator
}</
{{out}}
<pre>
| |||