Task: Bioinformatics_Sequence mutation


C++: #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;
}










Ada: with Ada.Containers.Vectors;
with Ada.Numerics.Discrete_Random;
with Ada.Text_Io;

procedure Mutations is

   Width : constant := 60;

   type Nucleotide_Type is (A, C, G, T);
   type Operation_Type is (Delete, Insert, Swap);
   type Position_Type is new Natural;

   package Position_Io   is new Ada.Text_Io.Integer_Io (Position_Type);
   package Nucleotide_Io is new Ada.Text_Io.Enumeration_Io (Nucleotide_Type);
   package Operation_Io  is new Ada.Text_Io.Enumeration_Io (Operation_Type);

   use Ada.Text_Io, Position_Io, Nucleotide_Io, Operation_Io;

   package Sequence_Vectors is new Ada.Containers.Vectors (Index_Type   => Position_Type,
                                                           Element_Type => Nucleotide_Type);
   package Nucleotide_Generators is new Ada.Numerics.Discrete_Random (Result_Subtype => Nucleotide_Type);
   package Operation_Generators  is new Ada.Numerics.Discrete_Random (Result_Subtype => Operation_Type);

   procedure Pretty_Print (Sequence : Sequence_Vectors.Vector) is
      First : Position_Type := Sequence.First_Index;
      Last  : Position_Type;
      Count : array (Nucleotide_Type) of Natural := (others  => 0);
   begin
      Last := Position_Type'Min (First + Width - 1,
                                 Sequence.Last_Index);
      loop
         Position_Io.Put (First, Width => 4);
         Put (": ");
         for N in First .. Last loop
            declare
               Nucleotide : Nucleotide_Type renames Sequence (N);
            begin
               Put (Nucleotide);
               Count (Nucleotide) := Count (Nucleotide) + 1;
            end;
         end loop;
         New_Line;
         exit when Last = Sequence.Last_Index;
         First := Last + 1;
         Last  := Position_Type'Min (First + Width - 1,
                                     Sequence.Last_Index);
      end loop;

      for N in Count'Range loop
         Put ("Count of "); Put (N); Put (" is "); Put (Natural'Image (Count (N))); New_Line;
      end loop;

   end Pretty_Print;

   function Random_Position (First, Last : Position_Type) return Position_Type is
      subtype Position_Range is Position_Type range First .. Last;
      package Position_Generators is new Ada.Numerics.Discrete_Random (Result_Subtype => Position_Range);
      Generator : Position_Generators.Generator;
   begin
      Position_Generators.Reset (Generator);
      return Position_Generators.Random (Generator);
   end Random_Position;

   Nucleotide_Generator : Nucleotide_Generators.Generator;
   Operation_Generator  : Operation_Generators.Generator;

   Sequence   : Sequence_Vectors.Vector;
   Position   : Position_Type;
   Nucleotide : Nucleotide_Type;
   Operation  : Operation_Type;
begin
   Nucleotide_Generators.Reset (Nucleotide_Generator);
   Operation_Generators.Reset (Operation_Generator);

   for A in 1 .. 200 loop
      Sequence.Append (Nucleotide_Generators.Random (Nucleotide_Generator));
   end loop;

   Put_Line ("Initial sequence:");
   Pretty_Print (Sequence);
   New_Line;

   Put_Line ("Mutations:");
   for Mutate in 1 .. 10 loop

      Operation := Operation_Generators.Random (Operation_Generator);
      case Operation is

         when Delete =>
            Position := Random_Position (Sequence.First_Index, Sequence.Last_Index);
            Sequence.Delete (Index => Position);
            Put (Operation); Put (" at position "); Put (Position, Width => 0); New_Line;

         when Insert =>
            Position   := Random_Position (Sequence.First_Index, Sequence.Last_Index + 1);
            Nucleotide := Nucleotide_Generators.Random (Nucleotide_Generator);
            Sequence.Insert (Before   => Position,
                             New_Item => Nucleotide);
            Put (Operation); Put (" "); Put (Nucleotide); Put (" at position ");
            Put (Position, Width => 0); New_Line;

         when Swap =>
            Position   := Random_Position (Sequence.First_Index, Sequence.Last_Index);
            Nucleotide := Nucleotide_Generators.Random (Nucleotide_Generator);
            Sequence.Replace_Element (Index    => Position,
                                      New_Item => Nucleotide);
            Put (Operation); Put (" at position "); Put (Position, Width => 0);
            Put (" to "); Put (Nucleotide); New_Line;

      end case;
   end loop;

   New_Line;
   Put_Line ("Mutated sequence:");
   Pretty_Print (Sequence);

end Mutations;