Bioinformatics/Sequence mutation
Given a string of characters A, C, G, and T representing a DNA sequence write a routine to mutate the sequence, (string) by:
- Choosing a random base position in the sequence.
- Mutate the sequence by doing one of either:
- Swap the base at that position by changing it to one of A, C, G, or T. (which has a chance of swapping the base for the same base)
- Delete the chosen base at the position.
- Insert another base randomly chosen from A,C, G, or T into the sequence at that position.
- Randomly generate a test DNA sequence of at least 200 bases
- "Pretty print" the sequence and a count of its size, and the count of each base in the sequence
- Mutate the sequence ten times.
- "Pretty print" the sequence after all mutations, and a count of its size, and the count of each base in the sequence.
You are encouraged to solve this task according to the task description, using any language you may know.
- Task
- Extra credit
- Give more information on the individual mutations applied.
- Allow mutations to be weighted and/or chosen.
Arturo
<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 ""</lang>
- Output:
------------------------------ 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
C
Adenine ( A ) is always swapped for Thymine ( T ) and vice versa. Similarly with Cytosine ( C ) and Guanine ( G ). <lang C>
- include<stdlib.h>
- include<stdio.h>
- include<time.h>
typedef struct genome{
char base; struct genome *next;
}genome;
typedef struct{
char mutation; int position;
}genomeChange;
typedef struct{
int adenineCount,thymineCount,cytosineCount,guanineCount;
}baseCounts;
genome *strand; baseCounts baseData; int genomeLength = 100, lineLength = 50;
int numDigits(int num){
int len = 1;
while(num>10){
num /= 10;
len++;
}
return len;
}
void generateStrand(){
int baseChoice = rand()%4, i; genome *strandIterator, *newStrand;
baseData.adenineCount = 0; baseData.thymineCount = 0; baseData.cytosineCount = 0; baseData.guanineCount = 0; strand = (genome*)malloc(sizeof(genome)); strand->base = baseChoice==0?'A':(baseChoice==1?'T':(baseChoice==2?'C':'G')); baseChoice==0?baseData.adenineCount++:(baseChoice==1?baseData.thymineCount++:(baseChoice==2?baseData.cytosineCount++:baseData.guanineCount++)); strand->next = NULL;
strandIterator = strand;
for(i=1;i<genomeLength;i++){
baseChoice = rand()%4;
newStrand = (genome*)malloc(sizeof(genome));
newStrand->base = baseChoice==0?'A':(baseChoice==1?'T':(baseChoice==2?'C':'G'));
baseChoice==0?baseData.adenineCount++:(baseChoice==1?baseData.thymineCount++:(baseChoice==2?baseData.cytosineCount++:baseData.guanineCount++));
newStrand->next = NULL;
strandIterator->next = newStrand;
strandIterator = newStrand;
}
}
genomeChange generateMutation(int swapWeight, int insertionWeight, int deletionWeight){
int mutationChoice = rand()%(swapWeight + insertionWeight + deletionWeight); genomeChange mutationCommand;
mutationCommand.mutation = mutationChoice<swapWeight?'S':((mutationChoice>=swapWeight && mutationChoice<swapWeight+insertionWeight)?'I':'D'); mutationCommand.position = rand()%genomeLength;
return mutationCommand;
}
void printGenome(){
int rows, width = numDigits(genomeLength), len = 0,i,j;
lineLength = (genomeLength<lineLength)?genomeLength:lineLength;
rows = genomeLength/lineLength + (genomeLength%lineLength!=0);
genome* strandIterator = strand;
printf("\n\nGenome : \n--------\n");
for(i=0;i<rows;i++){
printf("\n%*d%3s",width,len,":");
for(j=0;j<lineLength && strandIterator!=NULL;j++){
printf("%c",strandIterator->base);
strandIterator = strandIterator->next;
}
len += lineLength;
}
while(strandIterator!=NULL){
printf("%c",strandIterator->base);
strandIterator = strandIterator->next;
}
printf("\n\nBase Counts\n-----------");
printf("\n%*c%3s%*d",width,'A',":",width,baseData.adenineCount);
printf("\n%*c%3s%*d",width,'T',":",width,baseData.thymineCount);
printf("\n%*c%3s%*d",width,'C',":",width,baseData.cytosineCount);
printf("\n%*c%3s%*d",width,'G',":",width,baseData.guanineCount);
printf("\n\nTotal:%*d",width,baseData.adenineCount + baseData.thymineCount + baseData.cytosineCount + baseData.guanineCount);
printf("\n");
}
void mutateStrand(int numMutations, int swapWeight, int insertionWeight, int deletionWeight){
int i,j,width,baseChoice; genomeChange newMutation; genome *strandIterator, *strandFollower, *newStrand;
for(i=0;i<numMutations;i++){
strandIterator = strand;
strandFollower = strand;
newMutation = generateMutation(swapWeight,insertionWeight,deletionWeight);
width = numDigits(genomeLength);
for(j=0;j<newMutation.position;j++){
strandFollower = strandIterator;
strandIterator = strandIterator->next;
}
if(newMutation.mutation=='S'){
if(strandIterator->base=='A'){
strandIterator->base='T';
printf("\nSwapping A at position : %*d with T",width,newMutation.position);
}
else if(strandIterator->base=='A'){
strandIterator->base='T';
printf("\nSwapping A at position : %*d with T",width,newMutation.position);
}
else if(strandIterator->base=='C'){
strandIterator->base='G';
printf("\nSwapping C at position : %*d with G",width,newMutation.position);
}
else{
strandIterator->base='C';
printf("\nSwapping G at position : %*d with C",width,newMutation.position);
}
}
else if(newMutation.mutation=='I'){
baseChoice = rand()%4;
newStrand = (genome*)malloc(sizeof(genome));
newStrand->base = baseChoice==0?'A':(baseChoice==1?'T':(baseChoice==2?'C':'G'));
printf("\nInserting %c at position : %*d",newStrand->base,width,newMutation.position);
baseChoice==0?baseData.adenineCount++:(baseChoice==1?baseData.thymineCount++:(baseChoice==2?baseData.cytosineCount++:baseData.guanineCount++));
newStrand->next = strandIterator;
strandFollower->next = newStrand;
genomeLength++;
}
else{
strandFollower->next = strandIterator->next;
strandIterator->next = NULL;
printf("\nDeleting %c at position : %*d",strandIterator->base,width,newMutation.position);
free(strandIterator);
genomeLength--;
}
}
}
int main(int argc,char* argv[]) {
int numMutations = 10, swapWeight = 10, insertWeight = 10, deleteWeight = 10;
if(argc==1||argc>6){
printf("Usage : %s <Genome Length> <Optional number of mutations> <Optional Swapping weight> <Optional Insertion weight> <Optional Deletion weight>\n",argv[0]);
return 0;
}
switch(argc){
case 2: genomeLength = atoi(argv[1]);
break;
case 3: genomeLength = atoi(argv[1]);
numMutations = atoi(argv[2]);
break;
case 4: genomeLength = atoi(argv[1]);
numMutations = atoi(argv[2]);
swapWeight = atoi(argv[3]);
break;
case 5: genomeLength = atoi(argv[1]);
numMutations = atoi(argv[2]);
swapWeight = atoi(argv[3]);
insertWeight = atoi(argv[4]);
break;
case 6: genomeLength = atoi(argv[1]);
numMutations = atoi(argv[2]);
swapWeight = atoi(argv[3]);
insertWeight = atoi(argv[4]);
deleteWeight = atoi(argv[5]);
break;
};
srand(time(NULL)); generateStrand();
printf("\nOriginal:");
printGenome(); mutateStrand(numMutations,swapWeight,insertWeight,deleteWeight);
printf("\n\nMutated:"); printGenome();
return 0;
} </lang> Sample run :
C:\My Projects\networks>a 500 30 15 10 5 Original: Genome : -------- 0 :CGATGAGTTTCCTCCAAGGAGCAGGGCGTGACGGAAGGGAGGCTTAGGTC 50 :CGCATGCTCGTCGGCAGCCGGCTGGTGCCGTCGTAACCTTCACATTATTC 100 :TAGAATTTCGATGCACCTGATGACTCATACCCAGATGTAGGGGTACGCGA 150 :TGCAGATGCGGGCACGAGGAATTGTGGGCAAGCCGGCAGGTCTTTTGTAA 200 :GTTGTCACTAACTAAATAGAGGGATGGATGTTATAGCACACTACTGTCGA 250 :TTACGGACAGCGTCCCGATTCGTCATACGACCAGGATATATACTCGACGT 300 :CCAACAGGAGATTCACGTAGTGAACGCAGTTGACAGCCTGCTCGTATCTC 350 :CAGGGGTGGACTGCACCGTTCGTTAACTGCTGCCACATTAAACAGCTTCC 400 :CACTCCTTGACGCCAGACTCGGTACCACAGACCGTCAAGCTCCTATTTCC 450 :TTTGCAGTTAAAAAACACTATGGTGAAGGTCGGAGAGATGACCTCATCTA Base Counts ----------- A :124 T :118 C :126 G :132 Total:500 Inserting G at position : 205 Inserting G at position : 144 Inserting C at position : 171 Swapping A at position : 335 with T Inserting A at position : 101 Swapping C at position : 109 with G Swapping A at position : 306 with T Inserting G at position : 51 Swapping G at position : 1 with C Deleting G at position : 60 Swapping G at position : 66 with C Inserting C at position : 41 Inserting C at position : 425 Swapping C at position : 173 with G Inserting A at position : 319 Swapping G at position : 460 with C Deleting T at position : 61 Swapping C at position : 160 with G Inserting C at position : 251 Swapping G at position : 337 with C Inserting G at position : 43 Inserting T at position : 146 Inserting T at position : 181 Deleting G at position : 53 Deleting A at position : 464 Swapping G at position : 362 with C Swapping G at position : 190 with C Swapping C at position : 280 with G Inserting T at position : 479 Deleting C at position : 400 Mutated: Genome : -------- 0 :CCATGAGTTTCCTCCAAGGAGCAGGGCGTGACGGAAGGGAGCGGCTTAGG 50 :TCCGCATGCTCCGGCACCCGGCTGGTGCCGTCGTAACCTTCACATTATTC 100 :TAAGAATTTGGATGCACCTGATGACTCATACCCAGATGTAGGGGTTGACG 150 :CGATGCAGATGGGGGCACGAGGAGATTGTGTGGCAAGCCGCCAGGTCTTT 200 :TGTAAGTTGTGCACTAACTAAATAGAGGGATGGATGTTATAGCACACTAC 250 :TGTCCGATTACGGACAGCGTCCCGATTCGTGATACGACCAGGATATATAC 300 :TCGACGTCCTACAGGAGATTCAACGTAGTGAACGCAGTTCTCAGCCTGCT 350 :CGTATCTCCAGGCGTGGACTGCACCGTTCGTTAACTGCTGCCACATTAAA 400 :AGCTTCCCACTCCTTGACGCCAGACTCCGGTACCACAGACCGTCAAGCTC 450 :CTATTTCCTTTCCGTTAAAAAACACTATTGGTGAAGGTCGGAGAGATGAC 500 :CTCATCTA Base Counts ----------- A :126 T :121 C :130 G :136 Total:513
C++
<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;
}</lang>
- Output:
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
Common Lisp
Usage :
- (mutate (<Genome length> <Number of mutations>
- :ins_w <Insertion weight> :swp_w <Swap weight> :del_w <Delete weight>
- :genome <Genome Sequence>)
All keys are optional. <Genome length> is discarded when :genome is set. <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"))
</lang>
- Output:
[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
Factor
<lang factor>USING: assocs combinators.random formatting grouping io kernel macros math math.statistics namespaces prettyprint quotations random sequences sorting ; IN: sequence-mutation
SYMBOL: verbose? ! Turn on to show mutation details.
! Off by default.
! Return a random base as a character.
- rand-base ( -- n ) "ACGT" random ;
! Generate a random dna sequence of length n.
- <dna> ( n -- seq ) [ rand-base ] "" replicate-as ;
! Prettyprint a dna sequence in blocks of n.
- .dna ( seq n -- )
"SEQUENCE:" print [ group ] keep [ * swap " %3d: %s\n" printf ] curry each-index ;
! Show a histogram of bases in a dna sequence and their total.
- show-counts ( seq -- )
"BASE COUNTS:" print histogram >alist [ first ] sort-with [ [ " %c: %3d\n" printf ] assoc-each ] [ "TOTAL: " write [ second ] [ + ] map-reduce . ] bi ;
! Prettyprint the overall state of a dna sequence.
- show-dna ( seq -- ) [ 50 .dna nl ] [ show-counts nl ] bi ;
! Call a quotation only if verbose? is on.
- log ( quot -- ) verbose? get [ call ] [ drop ] if ; inline
! Set index n to a random base.
- bswap ( n seq -- seq' )
[ rand-base ] 2dip 3dup [ nth ] keepd spin [ " index %3d: swapping %c with %c\n" printf ] 3curry log [ set-nth ] keep ;
! Remove the base at index n.
- bdelete ( n seq -- seq' )
2dup dupd nth [ " index %3d: deleting %c\n" printf ] 2curry log remove-nth ;
! Insert a random base at index n.
- binsert ( n seq -- seq' )
[ rand-base ] 2dip over reach [ " index %3d: inserting %c\n" printf ] 2curry log insert-nth ;
! Allow "passing" probabilities to casep. This is necessary ! because casep is a macro. MACRO: build-casep-seq ( seq -- quot )
{ [ bswap ] [ bdelete ] [ binsert ] } zip 1quotation ;
! Mutate a dna sequence according to some weights. ! For example, ! "ACGT" { 0.1 0.3 0.6 } mutate ! means swap with 0.1 probability, delete with 0.3 probability, ! and insert with 0.6 probability.
- mutate ( dna-seq weights-seq -- dna-seq' )
[ [ length random ] keep ] [ build-casep-seq ] bi* casep ; inline
! Prettyprint a sequence of weights.
- show-weights ( seq -- )
"MUTATION PROBABILITIES:" print " swap: %.2f\n delete: %.2f\n insert: %.2f\n\n" vprintf ;
- main ( -- )
verbose? on "ORIGINAL " write 200 <dna> dup show-dna 10
{ 0.2 0.2 0.6 } dup show-weights "MUTATION LOG:" print
[ mutate ] curry times nl "MUTATED " write show-dna ;
MAIN: main</lang>
- Output:
ORIGINAL SEQUENCE:
0: CACAGGCAAGGGTCGTATGCTACTATAGATGTTTCAGAACCGTATTTCGA
50: CTCCGACGCGGTCATGAAGCAGACACTCCGTCACCGATTGCAAGTGTGCA
100: GTTGGGAGAATGCATTAAAATTCTGGGTTATGAAACGGGCAGCCTTGATT
150: GACAGGTGGTCCAGCGACAGTTTAACATACCAAACTCTTTGAGTACGCAG
BASE COUNTS:
A: 55
C: 44
G: 52
T: 49
TOTAL: 200
MUTATION PROBABILITIES:
swap: 0.20
delete: 0.20
insert: 0.60
MUTATION LOG:
index 82: deleting A
index 161: inserting C
index 48: deleting G
index 10: swapping G with T
index 184: swapping T with C
index 137: inserting T
index 60: inserting T
index 135: inserting C
index 32: inserting T
index 201: inserting A
MUTATED SEQUENCE:
0: CACAGGCAAGTGTCGTATGCTACTATAGATGTTTTCAGAACCGTATTTCA
50: CTCCGACGCGGTTCATGAAGCAGACACTCCGTCCCGATTGCAAGTGTGCA
100: GTTGGGAGAATGCATTAAAATTCTGGGTTATGAAACCGGGTCAGCCTTGA
150: TTGACAGGTGGTCCCAGCGACAGTTTAACATACCAAACCCTTTGAGTACG
200: CAAG
BASE COUNTS:
A: 55
C: 47
G: 50
T: 52
TOTAL: 204
Go
<lang go>package main
import (
"fmt" "math/rand" "sort" "time"
)
const bases = "ACGT"
// 'w' contains the weights out of 300 for each // of swap, delete or insert in that order. func mutate(dna string, w [3]int) string {
le := len(dna)
// get a random position in the dna to mutate
p := rand.Intn(le)
// get a random number between 0 and 299 inclusive
r := rand.Intn(300)
bytes := []byte(dna)
switch {
case r < w[0]: // swap
base := bases[rand.Intn(4)]
fmt.Printf(" Change @%3d %q to %q\n", p, bytes[p], base)
bytes[p] = base
case r < w[0]+w[1]: // delete
fmt.Printf(" Delete @%3d %q\n", p, bytes[p])
copy(bytes[p:], bytes[p+1:])
bytes = bytes[0 : le-1]
default: // insert
base := bases[rand.Intn(4)]
bytes = append(bytes, 0)
copy(bytes[p+1:], bytes[p:])
fmt.Printf(" Insert @%3d %q\n", p, base)
bytes[p] = base
}
return string(bytes)
}
// Generate a random dna sequence of given length. func generate(le int) string {
bytes := make([]byte, le)
for i := 0; i < le; i++ {
bytes[i] = bases[rand.Intn(4)]
}
return string(bytes)
}
// Pretty print dna and stats. func prettyPrint(dna string, rowLen int) {
fmt.Println("SEQUENCE:")
le := len(dna)
for i := 0; i < le; i += rowLen {
k := i + rowLen
if k > le {
k = le
}
fmt.Printf("%5d: %s\n", i, dna[i:k])
}
baseMap := make(map[byte]int) // allows for 'any' base
for i := 0; i < le; i++ {
baseMap[dna[i]]++
}
var bases []byte
for k := range baseMap {
bases = append(bases, k)
}
sort.Slice(bases, func(i, j int) bool { // get bases into alphabetic order
return bases[i] < bases[j]
})
fmt.Println("\nBASE COUNT:")
for _, base := range bases {
fmt.Printf(" %c: %3d\n", base, baseMap[base])
}
fmt.Println(" ------")
fmt.Println(" Σ:", le)
fmt.Println(" ======\n")
}
// Express weights as a string. func wstring(w [3]int) string {
return fmt.Sprintf(" Change: %d\n Delete: %d\n Insert: %d\n", w[0], w[1], w[2])
}
func main() {
rand.Seed(time.Now().UnixNano())
dna := generate(250)
prettyPrint(dna, 50)
muts := 10
w := [3]int{100, 100, 100} // use e.g. {0, 300, 0} to choose only deletions
fmt.Printf("WEIGHTS (ex 300):\n%s\n", wstring(w))
fmt.Printf("MUTATIONS (%d):\n", muts)
for i := 0; i < muts; i++ {
dna = mutate(dna, w)
}
fmt.Println()
prettyPrint(dna, 50)
}</lang>
- Output:
Sample run:
SEQUENCE:
0: AATCCAGAAGTTGCGGGAACCGTCGAATAGTGTTCATTAAGTGTCCCGCG
50: GAGTAGCCTCGTAATATAGAATGACCGGGCTTCCCAGCTAGACTTGTCCG
100: CCACGTTTGTGTAGGGCGCAGCGAGACTGCTCTTGATACTCGTTATGTTC
150: CTCACCGGATTATTGAATAGAGTCGAGGGGCTGACGTGACTGAACATTGC
200: CTCCTTTGCGACTAATCTTTCCTTCAATGAACAGGCGCTACCCGTCATCG
BASE COUNT:
A: 56
C: 63
G: 64
T: 67
------
Σ: 250
======
WEIGHTS (ex 300):
Change: 100
Delete: 100
Insert: 100
MUTATIONS (10):
Change @195 'A' to 'C'
Insert @ 95 'G'
Change @137 'T' to 'C'
Delete @207 'T'
Insert @148 'C'
Insert @113 'A'
Change @ 45 'C' to 'T'
Delete @ 93 'T'
Insert @ 51 'C'
Delete @248 'A'
SEQUENCE:
0: AATCCAGAAGTTGCGGGAACCGTCGAATAGTGTTCATTAAGTGTCTCGCG
50: GCAGTAGCCTCGTAATATAGAATGACCGGGCTTCCCAGCTAGACTGGTCC
100: GCCACGTTTGTGTAAGGGCGCAGCGAGACTGCTCTTGACACTCGTTATGC
150: TTCCTCACCGGATTATTGAATAGAGTCGAGGGGCTGACGTGACTGAACCT
200: TGCCTCCTTGCGACTAATCTTTCCTTCAATGAACAGGCGCTACCCGTCTC
250: G
BASE COUNT:
A: 55
C: 66
G: 65
T: 65
------
Σ: 251
======
Haskell
<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)</lang>
- Output:
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
J
<lang J>ACGT=: 'ACGT' MUTS=: ;: 'del ins mut'
NB. generate sequence of size y of uniformly selected nucleotides. NB. represent sequences as ints in range i.4 pretty printed. nuc NB. defined separately to avoid fixing value inside mutation NB. functions. nuc=: monad : '?4' dna=: nuc"0 @ i.
NB. randomly mutate nucleotide at a random index by deletion insertion NB. or mutation of a nucleotide. del=: {.,[:}.}. ins=: {.,nuc@],}. mut=: {.,nuc@],[:}.}.
NB. pretty print nucleotides in rows of 50 with numbering seq=: [: (;~ [: (4&":"0) 50*i.@#) _50]\{&ACGT
sim=: monad define 'n k ws'=. y NB. initial size, mutations, and weights for mutations ws=. (% +/) ws NB. normalize weights A=.0$]D0=.D=. dna n NB. initial dna and history of actions
NB. k times do a random action according to weights and record it for. i.k do.
D=.". action=. (":?#D),' ',(":MUTS{::~(+/\ws)I.?0),' D'
A=. action ; A
end.
echo 'actions';,. A-.a: echo ('mutation';'probability') , MUTS ,. <"0 ws ('start';'end'),.(seq D0) ,: seq D )
simulate=: (sim@(1 1 1&; &. |. ))`sim@.(3=#)</lang>
- Output:
simulate 200 ; 10 ┌─────────┐ │actions │ ├─────────┤ │60 mut D │ ├─────────┤ │156 del D│ ├─────────┤ │44 mut D │ ├─────────┤ │64 mut D │ ├─────────┤ │167 mut D│ ├─────────┤ │40 ins D │ ├─────────┤ │39 mut D │ ├─────────┤ │187 del D│ ├─────────┤ │186 del D│ ├─────────┤ │150 del D│ └─────────┘ ┌────────┬───────────┐ │mutation│probability│ ├────────┼───────────┤ │del │0.333333 │ ├────────┼───────────┤ │ins │0.333333 │ ├────────┼───────────┤ │mut │0.333333 │ └────────┴───────────┘ ┌─────┬────┬──────────────────────────────────────────────────┐ │start│ 0│GGCTGTTGGCCGCCAATCTACAATGATAGCGCGTGAGGAGGGCTAATGTA│ │ │ 50│GAGCCAATAATGGATGCTCGCGCTTCTGCTTATGCTGGTTACTGCTGCCC│ │ │ 100│AAAAACGGGGTACATTGAGCGATAAGCCCGCAAGGTTACTGCTCGTGACA│ │ │ 150│GTCCGAACACCACATTCGTGGTTACTCGACTCTGCCACCTCTTAGCGGAT│ ├─────┼────┼──────────────────────────────────────────────────┤ │end │ 0│GGCTGTTGGCCGCCAATCTACAATGATAGCGCGTGAGGACCGGCAAATGT│ │ │ 50│AGAGCCAATACTGGATGCTCGCGCTTCTGCTTATGCTGGTTACTGCTGCC│ │ │ 100│CAAAAACGGGGTACATTGAGCGATAAGCCCGCAAGGTTACTGCTCGTGAC│ │ │ 150│ATCCGACACCACATTCCTGGTTACTCGACTCTGCCACCTTAGCGGAT │ └─────┴────┴──────────────────────────────────────────────────┘ simulate 200 ; 10 ; 1 3 1 ┌─────────┐ │actions │ ├─────────┤ │120 ins D│ ├─────────┤ │199 ins D│ ├─────────┤ │138 mut D│ ├─────────┤ │15 ins D │ ├─────────┤ │8 del D │ ├─────────┤ │135 ins D│ ├─────────┤ │29 ins D │ ├─────────┤ │118 del D│ ├─────────┤ │111 ins D│ ├─────────┤ │10 del D │ └─────────┘ ┌────────┬───────────┐ │mutation│probability│ ├────────┼───────────┤ │del │0.2 │ ├────────┼───────────┤ │ins │0.6 │ ├────────┼───────────┤ │mut │0.2 │ └────────┴───────────┘ ┌─────┬────┬──────────────────────────────────────────────────┐ │start│ 0│GAACATACAATATCGTGTGGGTGGTAAGGTGCGCCGATTTGGCAGTGTAG│ │ │ 50│AGCGGCCTCTGGCCGGGCCCATACTGACATATCTTTTATCTCCGTGCTAG│ │ │ 100│CAGAAGAATCAAACGCGTCAAGATGCTGGCGCGGGCTGATATGCGCCCGG│ │ │ 150│CAGTGGAGAACTGCGTTGATACACCTCAAAGATAAGCGGACGATATTAGC│ ├─────┼────┼──────────────────────────────────────────────────┤ │end │ 0│GAACATACAATCGTGCTGGGTGGTAAGGTTGCGCCGATTTGGCAGTGTAG│ │ │ 50│AGCGGCCTCTGGCCGGGCCCATACTGACATATCTTTTATCTCCGTGCTAG│ │ │ 100│CAGAAGAATCAACACGCGTAGAGATGCTGGCGCGGGACTGATATGCGCCC│ │ │ 150│GGCAGTGGAGAACTGCGTTGATACACCTCAAAGATAAGCGGACGATATTA│ │ │ 200│GGC │ └─────┴────┴──────────────────────────────────────────────────┘
Java
<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'};
}</lang>
- Output:
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
JavaScript
<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); </lang>
- Output:
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
Julia
<lang julia>dnabases = ['A', 'C', 'G', 'T'] randpos(seq) = rand(1:length(seq)) # 1 mutateat(pos, seq) = (s = seq[:]; s[pos] = rand(dnabases); s) # 2-1 deleteat(pos, seq) = [seq[1:pos-1]; seq[pos+1:end]] # 2-2 randinsertat(pos, seq) = [seq[1:pos]; rand(dnabases); seq[pos+1:end]] # 2-3
function weightedmutation(seq, pos, weights=[1, 1, 1], verbose=true) # Extra credit
p, r = weights ./ sum(weights), rand()
f = (r <= p[1]) ? mutateat : (r < p[1] + p[2]) ? deleteat : randinsertat
verbose && print("Mutate by ", f == mutateat ? "swap" :
f == deleteat ? "delete" : "insert")
return f(pos, seq)
end
function weightedrandomsitemutation(seq, weights=[1, 1, 1], verbose=true)
position = randpos(seq)
newseq = weightedmutation(seq, position, weights, verbose)
verbose && println(" at position $position")
return newseq
end
randdnasequence(n) = rand(dnabases, n) # 3
function dnasequenceprettyprint(seq, colsize=50) # 4
println(length(seq), "nt DNA sequence:\n")
rows = [seq[i:min(length(seq), i + colsize - 1)] for i in 1:colsize:length(seq)]
for (i, r) in enumerate(rows)
println(lpad(colsize * (i - 1), 5), " ", String(r))
end
bases = [[c, 0] for c in dnabases]
for c in seq, base in bases
if c == base[1]
base[2] += 1
end
end
println("\nNucleotide counts:\n")
for base in bases
println(lpad(base[1], 10), lpad(string(base[2]), 12))
end
println(lpad("Other", 10), lpad(string(length(seq) - sum(x[2] for x in bases)), 12))
println(" _________________\n", lpad("Total", 10), lpad(string(length(seq)), 12))
end
function testbioseq()
sequence = randdnasequence(500)
dnasequenceprettyprint(sequence)
for _ in 1:10 # 5
sequence = weightedrandomsitemutation(sequence)
end
println("\n Mutated:"); dnasequenceprettyprint(sequence) # 6
end
testbioseq()
</lang>
- Output:
500nt DNA sequence:
0 TCACGTAACAGAGGTATAGTTGATCTTGAGCGGGCTGGCTCCCGGGTTTC
50 TAGCAAGAAAAGGGGAGGGAAGTGCGCCTGCTTTTGCCCCGGGCACCCCA
100 ATCGAAGACAGCTCCGGGGTCGCACATTTTTATGGCCACATAATGAGGGA
150 ATGCACGCATCACTCCTATCACTAACTGCGAACTCATGTGACTGTGCAAA
200 ACACCTTTAACACTGCGATGCCGTGGGGACGGGCCCCCCCAGCGGTATAG
250 CGCGCACACGCGACAGATGTTAACTCGAATGGTCGCGCCGGGGAGTGCAC
300 CCCTTGACATATACTCCAGATGCAATGCGCTATACTTTATGAACTTGCAT
350 AAGCTGCGCAGGGGGGATTGACTTATACTACATATTAACTACCGATATCG
400 ACGCAAATATTCGGGCGGTCTAAAGTGTGTCAGAACGGACATGCCGCCCA
450 GAATCACGGCTACTGAGGACAAATACGCATTCCCGGTGCTGCATTCATTC
Nucleotide counts:
A 127
C 133
G 131
T 109
Other 0
_________________
Total 500
Mutate by swap at position 253
Mutate by swap at position 448
Mutate by insert at position 379
Mutate by delete at position 311
Mutate by delete at position 335
Mutate by insert at position 132
Mutate by swap at position 191
Mutate by swap at position 481
Mutate by insert at position 189
Mutate by insert at position 423
Mutated:
502nt DNA sequence:
0 TCACGTAACAGAGGTATAGTTGATCTTGAGCGGGCTGGCTCCCGGGTTTC
50 TAGCAAGAAAAGGGGAGGGAAGTGCGCCTGCTTTTGCCCCGGGCACCCCA
100 ATCGAAGACAGCTCCGGGGTCGCACATTTTTACTGGCCACATAATGAGGG
150 AATGCACGCATCACTCCTATCACTAACTGCGAACTCATGATCACTGTGCA
200 AAACACCTTTAACACTGCGATGCCGTGGGGACGGGCCCCCCCAGCGGTAT
250 AGCGAGCACACGCGACAGATGTTAACTCGAATGGTCGCGCCGGGGAGTGC
300 ACCCCTTGACATTACTCCAGATGCAATGCGCTATACTTATGAACTTGCAT
350 AAGCTGCGCAGGGGGGATTGACTTATACTGACATATTAACTACCGATATC
400 GACGCAAATATTCGGGCGGTCTAGAAGTGTGTCAGAACGGACATGCCGCT
450 CAGAATCACGGCTACTGAGGACAAATACGCATTCCCGGTGCTGCATTCAT
500 TC
Nucleotide counts:
A 128
C 133
G 132
T 109
Other 0
_________________
Total 502
Mathematica / Wolfram Language
BioSequence is a fundamental data type in Mathematica: <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"]]]</lang>
- Output:
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}}
Nim
<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()</lang>
- Output:
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
//
Perl
<lang perl>use strict; use warnings; use feature 'say';
my @bases = <A C G T>;
my $dna; $dna .= $bases[int rand 4] for 1..200;
my %cnt; $cnt{$_}++ for split //, $dna;
sub pretty {
my($string) = @_;
my $chunk = 10;
my $wrap = 5 * ($chunk+1);
($string =~ s/(.{$chunk})/$1 /gr) =~ s/(.{$wrap})/$1\n/gr;
}
sub mutate {
my($dna,$count) = @_; my $orig = $dna; substr($dna,rand length $dna,1) = $bases[int rand 4] while $count > diff($orig, $dna) =~ tr/acgt//; $dna
}
sub diff {
my($orig, $repl) = @_;
for my $i (0 .. -1+length $orig) {
substr($repl,$i,1, lc substr $repl,$i,1) if substr($orig,$i,1) ne substr($repl,$i,1);
}
$repl;
}
say "Original DNA strand:\n" . pretty($dna); say "Total bases: ". length $dna; say "$_: $cnt{$_}" for @bases;
my $mutate = mutate($dna, 10); %cnt = (); $cnt{$_}++ for split //, $mutate; say "\nMutated DNA strand:\n" . pretty diff $dna, $mutate; say "Total bases: ". length $mutate; say "$_: $cnt{$_}" for @bases; </lang>
- Output:
Original DNA strand: TGGAACATGT CCCAACGAGT TCTTCTTGCT AGCAGATTTT TTCAGTTGAT CGTCACATGC GGTAGACTAC CCAAGGTGTG ACTACTCGCA TGCCTGATCT AAATGGACAG TCGGCAGGCT AGTGCTAATT ACCGGAAGTA CGAACGAGCC ATGCTGAGCG ACTCATCATT GTGAAATCGA GCCTATCTGC ATGACCTAAT Total bases: 200 A: 52 C: 48 G: 47 T: 53 Mutated DNA strand: TGGAACATGT CCCAACGAGT cCTTCTTGCT AGCcGATTTT TTCAGTTGgT gGTCACATGC aGTAGACTAC CCgAGGTGTG ACTACTCGCA TGCCTGATCT AAATGGACAG TCGGCAGGCT AGTGCTAATT ACCGGAAGTA CGAACGAGCt ATGCaGAGCG ACTCATCgTT GTGAAATCGA GCCTATCTGC AgGACCTAAT Total bases: 200 A: 50 C: 48 G: 51 T: 51
Phix
string dna = repeat(' ',200+rand(300)) for i=1 to length(dna) do dna[i] = "ACGT"[rand(4)] end for procedure show() sequence acgt = repeat(0,5) for i=1 to length(dna) do acgt[find(dna[i],"ACGT")] += 1 end for acgt[$] = sum(acgt) sequence s = split(trim(join_by(split(join_by(dna,1,10,""),"\n"),1,5," ")),"\n") for i=1 to length(s) do printf(1,"%3d: %s\n",{(i-1)*50+1,s[i]}) end for printf(1,"\nBase counts: A:%d, C:%d, G:%d, T:%d, total:%d\n",acgt) end procedure procedure mutate() printf(1,"\n") for i=1 to 10 do integer p = rand(length(dna)), sdi = "SDI"[rand(3)], rep = "ACGT"[rand(4)], was = dna[p] switch sdi do case 'S':dna[p] = rep printf(1,"swapped %c at %d for %c\n",{was,p,rep}) case 'D':dna[p..p] = "" printf(1,"deleted %c at %d\n",{was,p}) case 'I':dna[p..p-1] = ""&rep printf(1,"inserted %c at %d, before %c\n",{rep,p,was}) end switch end for printf(1,"\n") end procedure show() mutate() show()
- Output:
1: ATAGACCGAT GTGTAGGTCT CGAACATCCC TGGGGTAGCT CAGCTTGGGG 51: GTTGACCTGT CTTGCTCCCA TGAACTGAGG GATTTGGAAA TAACGCTTAT 101: AACTGCGGGG GATTGATATG GGACATTGTT GCTGTAGGGC TTCGGCGTGC 151: TTAGAAACAA GAGAACACCA ATTTCGATAG ACCAGGTTTC GTCCCGCTAC 201: GAGTGATAGT AGCGCGTTAG GATTAATAAT CAGGGAGAGC ATTAAACATT 251: CTAAAAACTG ACATTCCCGA GGTGGAACCC GAGTTGATAA CGAGTATGCT 301: CTGAAAAATT AATTGATTGA TCCGCGACAC TATCACACCG TCTTCGCCGT 351: TGTAATGCAT GCTGGCTTAG CATCCGGATG CTCTTCTACC GATCTTAAGG 401: CGCGCACTCC CCAAGGAGCA TAGAAGCATC CCCGGCCCTC GACAGAGTCT 451: CCCAGTGTAA GTGTCTTTAT CCAAAATC Base counts: A:125, C:111, G:120, T:122, total:478 inserted C at 58, before T deleted T at 2 deleted C at 169 deleted G at 80 inserted A at 331, before T swapped C at 27 for T inserted A at 22, before A inserted T at 190, before G swapped C at 195 for C inserted A at 274, before G 1: AAGACCGATG TGTAGGTCTC GAAACATTCC TGGGGTAGCT CAGCTTGGGG 51: GTTGACCCTG TCTTGCTCCC ATGAACTGAG GATTTGGAAA TAACGCTTAT 101: AACTGCGGGG GATTGATATG GGACATTGTT GCTGTAGGGC TTCGGCGTGC 151: TTAGAAACAA GAGAACACAA TTTCGATAGA CCAGGTTTCT GTCCCGCTAC 201: GAGTGATAGT AGCGCGTTAG GATTAATAAT CAGGGAGAGC ATTAAACATT 251: CTAAAAACTG ACATTCCCGA GGTAGGAACC CGAGTTGATA ACGAGTATGC 301: TCTGAAAAAT TAATTGATTG ATCCGCGACA CTAATCACAC CGTCTTCGCC 351: GTTGTAATGC ATGCTGGCTT AGCATCCGGA TGCTCTTCTA CCGATCTTAA 401: GGCGCGCACT CCCCAAGGAG CATAGAAGCA TCCCCGGCCC TCGACAGAGT 451: CTCCCAGTGT AAGTGTCTTT ATCCAAAATC Base counts: A:128, C:110, G:119, T:123, total:480
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.
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.
<lang python>import random from collections import Counter
def basecount(dna):
return sorted(Counter(dna).items())
def seq_split(dna, n=50):
return [dna[i: i+n] for i in range(0, len(dna), n)]
def seq_pp(dna, n=50):
for i, part in enumerate(seq_split(dna, n)):
print(f"{i*n:>5}: {part}")
print("\n BASECOUNT:")
tot = 0
for base, count in basecount(dna):
print(f" {base:>3}: {count}")
tot += count
base, count = 'TOT', tot
print(f" {base:>3}= {count}")
def seq_mutate(dna, count=1, kinds="IDSSSS", choice="ATCG" ):
mutation = []
k2txt = dict(I='Insert', D='Delete', S='Substitute')
for _ in range(count):
kind = random.choice(kinds)
index = random.randint(0, len(dna))
if kind == 'I': # Insert
dna = dna[:index] + random.choice(choice) + dna[index:]
elif kind == 'D' and dna: # Delete
dna = dna[:index] + dna[index+1:]
elif kind == 'S' and dna: # Substitute
dna = dna[:index] + random.choice(choice) + dna[index+1:]
mutation.append((k2txt[kind], index))
return dna, mutation
if __name__ == '__main__':
length = 250
print("SEQUENCE:")
sequence = .join(random.choices('ACGT', weights=(1, 0.8, .9, 1.1), k=length))
seq_pp(sequence)
print("\n\nMUTATIONS:")
mseq, m = seq_mutate(sequence, 10)
for kind, index in m:
print(f" {kind:>10} @{index}")
print()
seq_pp(mseq)</lang>
- Output:
SEQUENCE:
0: GGAAGATTAGGTCACGGGCCTCATCTTGTGCGAGATAAATAATAACACTC
50: AGCGATCATTAGAATGTATATTGTACGGGCATGTTTATCTACCATAGGTC
100: CTGTCAAAAGATGGCTAGCTGCAATTTTTTCTTCTAGATCCCGATTACTG
150: CGGTATTTTTGTATAACGTGCTAAACGGTGTGTTTTCAGGTCGGCCTGCT
200: AATCTAACGCCAGTGGACTTGGGATGGACGCCCAACAACTGAGAGCGCGG
BASECOUNT:
A: 64
C: 51
G: 62
T: 73
TOT= 250
MUTATIONS:
Substitute @138
Substitute @72
Insert @103
Insert @129
Insert @124
Delete @52
Delete @202
Substitute @200
Insert @158
Delete @32
0: GGAAGATTAGGTCACGGGCCTCATCTTGTGCGGATAAATAATAACACTCA
50: GGATCATTAGAATGTATATTATACGGGCATGTTTATCTACCATAGGTCCT
100: GCTCAAAAGATGGCTAGCTGCAGATTTTGTTCTTCTAGAGCCCGATTACT
150: GCGGTATGTTTTGTATAACGTGCTAAACGGTGTGTTTTCAGGTCGGCCTG
200: CTATCTAACGCCAGTGGACTTGGGATGGACGCCCAACAACTGAGAGCGCG
250: G
BASECOUNT:
A: 63
C: 51
G: 65
T: 72
TOT= 251
Quackery
prettyprint and tallybases are defined at Bioinformatics/base count#Quackery.
<lang Quackery> [ $ "ACGT" 4 random peek ] is randomgene ( --> c )
[ $ "" swap times
[ randomgene join ] ] is randomsequence ( --> $ )
[ 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</lang>
- Output:
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
Racket
<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))</lang>
- Output:
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
Raku
(formerly Perl 6)
Unweighted mutations at this point. The mutated DNA strand has a "diff" operation performed on it which (in this specific case) renders the mutated base in lower case so it may be picked out more easily.
<lang perl6>my @bases = <A C G T>;
- The DNA strand
my $dna = @bases.roll(200).join;
- The Task
put "ORIGINAL DNA STRAND:"; put pretty $dna; put "\nTotal bases: ", +my $bases = $dna.comb.Bag; put $bases.sort( ~*.key ).join: "\n";
put "\nMUTATED DNA STRAND:"; my $mutate = $dna.&mutate(10); put pretty diff $dna, $mutate; put "\nTotal bases: ", +my $mutated = $mutate.comb.Bag; put $mutated.sort( ~*.key ).join: "\n";
- Helper subs
sub pretty ($string, $wrap = 50) {
$string.comb($wrap).map( { sprintf "%8d: %s", $++ * $wrap, $_ } ).join: "\n"
}
sub mutate ($dna is copy, $count = 1) {
$dna.substr-rw((^$dna.chars).roll, 1) = @bases.roll for ^$count; $dna
}
sub diff ($orig, $repl) {
($orig.comb Z $repl.comb).map( -> ($o, $r) { $o eq $r ?? $o !! $r.lc }).join
}</lang>
- Output:
ORIGINAL DNA STRAND:
0: ACGGATAGACCGTTCCTGCAAGCTGGTACGGTTCGAATGTTGACCTTATT
50: CTCCGCAGCGCACTACCCGATCGGGTAACGTACTCTATATGATGCCTATT
100: TTCCCCGCCTTACATCGGCGATCAATGTTCTTTTACGCTAACTAGGCGCA
150: CGTCGTGCCTTACCGAGAGCCAGTTCGAAATCGTGCTGAAAATATCTGGA
Total bases: 200
A 45
C 55
G 45
T 55
MUTATED DNA STRAND:
0: ACGGATAGcCCGTTCCTGCAAGCTGGTACGGTTCGAATGTTGACCTTATT
50: CTCCGCAGCGCACTACCCGATCGGGTcACtcACTCTATATGAcGCCTAaT
100: TTCCCCGCCTTACATCGGCGATCAATGTTCTTTTACGCTAACTAGGCGCA
150: CGTCGTGCCTTACCcAGAGCCAGTTCGAAATCGTGCTGAAAATATCTGGA
Total bases: 200
A 44
C 60
G 43
T 53
Ring
<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
</lang>
- Output:
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
Swift
<lang swift>let bases: [Character] = ["A", "C", "G", "T"]
enum Action: CaseIterable {
case swap, delete, insert
}
@discardableResult func mutate(dna: inout String) -> Action {
guard let i = dna.indices.shuffled().first(where: { $0 != dna.endIndex }) else {
fatalError()
}
let action = Action.allCases.randomElement()!
switch action {
case .swap:
dna.replaceSubrange(i..<i, with: [bases.randomElement()!])
case .delete:
dna.remove(at: i)
case .insert:
dna.insert(bases.randomElement()!, at: i)
}
return action
}
var d = ""
for _ in 0..<200 {
d.append(bases.randomElement()!)
}
func printSeq(_ dna: String) {
for startI in stride(from: 0, to: dna.count, by: 50) {
print("\(startI): \(dna.dropFirst(startI).prefix(50))")
}
print()
print("Size: \(dna.count)")
print()
let counts = dna.reduce(into: [:], { $0[$1, default: 0] += 1 })
for (char, count) in counts.sorted(by: { $0.key < $1.key }) {
print("\(char): \(count)")
}
}
printSeq(d)
print()
for _ in 0..<20 {
mutate(dna: &d)
}
printSeq(d)</lang>
- Output:
0: CCCTGTTACCCTTAAGTCACAAATCATGATAAGCAGCCTTCGAGCACTTC 50: GTGTCAAGCCTGATTCGAGCGCGCCGGTCATCCTCCGATAGAGCACGGGG 100: ACGCCCGCACTACCCCACTGGCGCTTGGTCGCTGAATAGGGCGCCCTTGG 150: TGGTGGATGGTCTTAAGCTGTCGCAAATCTAGCCCCGACCAAGAGAAGGC Size: 200 A: 43 C: 62 G: 54 T: 41 0: CCCTGTTACCCTTAAGTCACAAATCATGTATAAAGCAGCCTTCGAGCACT 50: TCGTGTCAAGCCTGATTCGAGCGCGCTAGGGCATCCTCCGTATAAGAGCA 100: CCGGGGACGCCCGCACTTACCACCACTGGCGCTTGGTCGCGAATAGGGGC 150: GCCCTTTGGTGGTGGATTGGTCTTAAGTGTCGCAAATCTAGCCCCCGACC 200: AAGAGAAGGC Size: 210 A: 47 C: 62 G: 56 T: 45
Wren
<lang ecmascript>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)</lang>
- Output:
Sample run:
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
======
zkl
<lang zkl>var [const] bases="ACGT", lbases=bases.toLower(); dna:=(190).pump(Data().howza(3),(0).random.fp(0,4),bases.get); // bucket of bytes
foreach s,m in (T("Original","Mutated").zip(T(True,False))){
println("\n",s," DNA strand:"); dnaPP(dna);
println("Base Counts: ", dna.len()," : ",
dna.text.toUpper().counts() // ("A",5, "C",10, ...)
.pump(String,Void.Read,"%s(%d) ".fmt));
if(m) mutate(dna,10,True);
}
fcn mutate(dna,count=1,verbose=False){
if(verbose) println("Mutating:");
do(count){
n,rb := (0).random(dna.len()), lbases[(0).random(4)];
switch( (0).random(3) ){
case(0){ if(verbose) println("Change[%d] '%s' to '%s'".fmt(n,dna.charAt(n),rb)); dna[n]=rb; } case(1){ if(verbose) println("Delete[%d] '%s'".fmt(n,dna.charAt(n))); dna.del(n); } else{ if(verbose) println("Insert[%d] '%s'".fmt(n,rb)); dna.insert(n,rb); }
} }
}
fcn dnaPP(dna,N=50){
[0..*,50].zipWith(fcn(n,bases){ println("%6d: %s".fmt(n,bases.concat())) },
dna.walker().walk.fp(50)).pump(Void); // .pump forces the iterator
}</lang>
- Output:
Original DNA strand:
0: AACGACAGGTTCTCGATGCGTGTCTTCACACATGTGGAGTCGCCAAGGAT
50: TGTTGATCAATGCGTAAACGTCTCCACGGGATACACGGGCAGCTTGCGGT
100: GACGAGTGCGGACCACCAAAAAAGGTGGGATCCACGTTGAGGAGCCTCAC
150: TACCTACGGCGTGATATGGCGGCAGGAGTCAAAAACTGCT
Base Counts: 190 : A(49) C(46) G(57) T(38)
Mutating:
Insert[123] 'c'
Insert[69] 't'
Delete[5] 'C'
Delete[147] 'T'
Change[167] 'G' to 't'
Change[153] 'C' to 'c'
Insert[151] 't'
Insert[156] 't'
Delete[150] 'T'
Change[102] 'C' to 'g'
Mutated DNA strand:
0: AACGAAGGTTCTCGATGCGTGTCTTCACACATGTGGAGTCGCCAAGGATT
50: GTTGATCAATGCGTAAACtGTCTCCACGGGATACACGGGCAGCTTGCGGT
100: GAgGAGTGCGGACCACCAAAAAAcGGTGGGATCCACGTTGAGGAGCCCAC
150: tACcTtACGGCGTGATATtGCGGCAGGAGTCAAAAACTGCT
Base Counts: 191 : A(49) C(45) G(57) T(40)
Rust
<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);
} </lang>
- Output:
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