Bioinformatics/Sequence mutation: Difference between revisions
Ada version
Alextretyak (talk | contribs) (Added 11l) |
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TOT= 249
</pre>
=={{header|Ada}}==
<lang Ada>with Ada.Containers.Vectors;
with Ada.Numerics.Discrete_Random;
with Ada.Text_Io;
procedure Mutations is
Width : constant := 60;
type Nucleotide_Type is (A, C, G, T);
type Operation_Type is (Delete, Insert, Swap);
type Position_Type is new Natural;
package Position_Io is new Ada.Text_Io.Integer_Io (Position_Type);
package Nucleotide_Io is new Ada.Text_Io.Enumeration_Io (Nucleotide_Type);
package Operation_Io is new Ada.Text_Io.Enumeration_Io (Operation_Type);
use Ada.Text_Io, Position_Io, Nucleotide_Io, Operation_Io;
package Sequence_Vectors is new Ada.Containers.Vectors (Index_Type => Position_Type,
Element_Type => Nucleotide_Type);
package Nucleotide_Generators is new Ada.Numerics.Discrete_Random (Result_Subtype => Nucleotide_Type);
package Operation_Generators is new Ada.Numerics.Discrete_Random (Result_Subtype => Operation_Type);
procedure Pretty_Print (Sequence : Sequence_Vectors.Vector) is
First : Position_Type := Sequence.First_Index;
Last : Position_Type;
Count : array (Nucleotide_Type) of Natural := (others => 0);
begin
Last := Position_Type'Min (First + Width - 1,
Sequence.Last_Index);
loop
Position_Io.Put (First, Width => 4);
Put (": ");
for N in First .. Last loop
declare
Nucleotide : Nucleotide_Type renames Sequence (N);
begin
Put (Nucleotide);
Count (Nucleotide) := Count (Nucleotide) + 1;
end;
end loop;
New_Line;
exit when Last = Sequence.Last_Index;
First := Last + 1;
Last := Position_Type'Min (First + Width - 1,
Sequence.Last_Index);
end loop;
for N in Count'Range loop
Put ("Count of "); Put (N); Put (" is "); Put (Natural'Image (Count (N))); New_Line;
end loop;
end Pretty_Print;
function Random_Position (First, Last : Position_Type) return Position_Type is
subtype Position_Range is Position_Type range First .. Last;
package Position_Generators is new Ada.Numerics.Discrete_Random (Result_Subtype => Position_Range);
Generator : Position_Generators.Generator;
begin
Position_Generators.Reset (Generator);
return Position_Generators.Random (Generator);
end Random_Position;
Nucleotide_Generator : Nucleotide_Generators.Generator;
Operation_Generator : Operation_Generators.Generator;
Sequence : Sequence_Vectors.Vector;
Position : Position_Type;
Nucleotide : Nucleotide_Type;
Operation : Operation_Type;
begin
Nucleotide_Generators.Reset (Nucleotide_Generator);
Operation_Generators.Reset (Operation_Generator);
for A in 1 .. 200 loop
Sequence.Append (Nucleotide_Generators.Random (Nucleotide_Generator));
end loop;
Put_Line ("Initial sequence:");
Pretty_Print (Sequence);
New_Line;
Put_Line ("Mutations:");
for Mutate in 1 .. 10 loop
Operation := Operation_Generators.Random (Operation_Generator);
case Operation is
when Delete =>
Position := Random_Position (Sequence.First_Index, Sequence.Last_Index);
Sequence.Delete (Index => Position);
Put (Operation); Put (" at position "); Put (Position, Width => 0); New_Line;
when Insert =>
Position := Random_Position (Sequence.First_Index, Sequence.Last_Index + 1);
Nucleotide := Nucleotide_Generators.Random (Nucleotide_Generator);
Sequence.Insert (Before => Position,
New_Item => Nucleotide);
Put (Operation); Put (" "); Put (Nucleotide); Put (" at position ");
Put (Position, Width => 0); New_Line;
when Swap =>
Position := Random_Position (Sequence.First_Index, Sequence.Last_Index);
Nucleotide := Nucleotide_Generators.Random (Nucleotide_Generator);
Sequence.Replace_Element (Index => Position,
New_Item => Nucleotide);
Put (Operation); Put (" at position "); Put (Position, Width => 0);
Put (" to "); Put (Nucleotide); New_Line;
end case;
end loop;
New_Line;
Put_Line ("Mutated sequence:");
Pretty_Print (Sequence);
end Mutations;</lang>
{{out}}
<pre>Initial sequence:
0: GCTGAGTCCGAATTAGTATTCATGAGATACGCATGTCAGTACGGCGACGACACGGGAAGA
60: GCAGATGAAAACTACTGGGGAGCTACCGAGCTGCCGTCGATTGTACGGATGTTATATTTC
120: CCATAGAACTACGAAGTTTTAGGATCCTTTCGGCGATGTGATAAGCAGGTATCAGTAGTA
180: AGCGAAGCGTTGACGTTTTT
Count of A is 55
Count of C is 37
Count of G is 56
Count of T is 52
Mutations:
DELETE at position 129
SWAP at position 172 to T
SWAP at position 28 to T
INSERT A at position 193
DELETE at position 164
SWAP at position 165 to G
DELETE at position 91
INSERT A at position 169
INSERT C at position 72
DELETE at position 146
Mutated sequence:
0: GCTGAGTCCGAATTAGTATTCATGAGATTCGCATGTCAGTACGGCGACGACACGGGAAGA
60: GCAGATGAAAACCTACTGGGGAGCTACCGAGCGCCGTCGATTGTACGGATGTTATATTTC
120: CCATAGAACACGAAGTTTTAGGATCCTTCGGCGATGTGATAAGAGGTATACTGTAGTAAG
180: CGAAGCGTTGACAGTTTTT
Count of A is 55
Count of C is 37
Count of G is 56
Count of T is 51</pre>
=={{header|Arturo}}==
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