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Ingy döt Net 2026-02-01 16:33:20 -08:00
parent 5150844a7d
commit 4bb20c9b71
7735 changed files with 38060 additions and 199180 deletions
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117
Task/Bioinformatics-Sequence-mutation/Ada/bioinformatics-sequence-mutation.ada
View file

@ -1,117 +0,0 @@
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;

20
Task/Bioinformatics-Sequence-mutation/Arturo/bioinformatics-sequence-mutation.arturo
View file

@ -9,12 +9,12 @@ prettyPrint: function [in][
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 []
case ch [
"A" -> count\A: count\A + 1
"T" -> count\T: count\T + 1
"G" -> count\G: count\G + 1
"C" -> count\C: count\C + 1
]
]
]
print ["Total count => A:" count\A, "T:" count\T "G:" count\G "C:" count\C]
@ -25,21 +25,21 @@ performRandomModifications: function [seq,times][
loop times [x][
what: random 1 3
case [what=]
when? -> 1 [
case what [
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 [
2 [
ind: random 0 (size result)
next: sample bases
result: insert result ind next
print ["inserting base" next "at position" ind]
]
else [
any [
ind: random 0 (size result)
previous: get result ind
result: remove result .index ind