Bioinformatics/Sequence mutation: Difference between revisions

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TOT= 251</pre>
TOT= 251</pre>

=={{header|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>

{{out}}

<pre>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</pre>


=={{header|zkl}}==
=={{header|zkl}}==

Revision as of 18:46, 3 March 2020

Task
Bioinformatics/Sequence mutation
You are encouraged to solve this task according to the task description, using any language you may know.
Task

Given a string of characters A, C, G, and T representing a DNA sequence write a routine to mutate the sequence, (string) by:

  1. Choosing a random base position in the sequence.
  2. Mutate the sequence by doing one of either:
    1. 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)
    2. Delete the chosen base at the position.
    3. Insert another base randomly chosen from A,C, G, or T into the sequence at that position.
  3. Randomly generate a test DNA sequence of at least 200 bases
  4. "Pretty print" the sequence and a count of its size, and the count of each base in the sequence
  5. Mutate the sequence ten times.
  6. "Pretty print" the sequence after all mutations, and a count of its size, and the count of each base in the sequence.
Extra credit
  • Give more information on the individual mutations applied.
  • Allow mutations to be weighted and/or chosen.

C

Adenine ( A ) is always swapped for Thymine ( T ) and vice versa. Similarly with Cytosine ( C ) and Guanine ( G ). <lang C>

  1. include<stdlib.h>
  2. include<stdio.h>
  3. 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

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
    ======

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

Perl

Translation of: Perl 6

<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

Perl 6

Works with: Rakudo version 2019.07.1

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>;

  1. The DNA strand

my $dna = @bases.roll(200).join;


  1. 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";


  1. 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

Phix

<lang 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\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()</lang>

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

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

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)
Retrieved from "https://rosettacode.org/wiki/Bioinformatics/Sequence_mutation?oldid=296359"