Bioinformatics/Subsequence: Difference between revisions
Ada version
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Write a routine to find all the positions of a randomly generated subsequence (four letters).
<br><br>
=={{header|Ada}}==
<lang Ada>with Ada.Text_Io;
with Ada.Strings.Fixed;
with Ada.Numerics.Discrete_Random;
procedure Sub_Sequence is
type Nucleotide is (A, C, G, T);
function To_Character (N : Nucleotide) return Character
is (case N is
when A => 'A', when C => 'C',
when G => 'G', when T => 'T');
package Random_Nucleotide is new Ada.Numerics.Discrete_Random (Nucleotide);
use Random_Nucleotide;
package Position_Io is new Ada.Text_Io.Integer_Io (Natural);
use Ada.Text_Io;
procedure Put_Bases (Seq : String; Width : Positive) is
First : Natural := Seq'First;
begin
while First < Seq'Last loop
declare
Last : constant Natural :=
Natural'Min (First + Width - 1, Seq'Last);
begin
Position_Io.Put (First); Put ("..");
Position_Io.Put (Last); Put (" ");
Put (Seq (First .. Last));
New_Line;
First := Last + 1;
end;
end loop;
end Put_Bases;
Gen : Generator;
Sequence : String (1 .. 405);
Substring : String (1 .. 4);
Pos : Natural := 0;
begin
Position_Io.Default_Width := 3;
Reset (Gen);
Sequence := (others => To_Character (Random (Gen)));
Substring := (others => To_Character (Random (Gen)));
Put_Line ("Search sequence:");
Put_Bases (Sequence, Width => 50);
New_Line;
Put ("Substring to search: ");
Put (Substring);
New_Line;
loop
Pos := Ada.Strings.Fixed.Index (Sequence, Substring, Pos + 1);
exit when Pos = 0;
Put ("Found at position: ");
Position_Io.Put (Pos); Put ("..");
Position_Io.Put (Pos + Substring'Length - 1);
New_Line;
end loop;
end Sub_Sequence;</lang>
{{out}}
<pre>Search sequence:
1.. 50 CCTACGGAAAAGTGATAAGGACAGATACATAATCCTAAAACCCTGGAAAA
51..100 CTTGTCTCGCCAGAGTAGGGCTCGGCAGGGGGGGCAGTGTTTTAAAACGT
101..150 CAGAGAATAGGCTCTACCTTGTTAGACTGCGAGTACTGGAGCGTAGTTCC
151..200 TATATTGCAAGCTGCTACAGTAAGTATCAAAGTATGCCACACATCCTTCT
201..250 ACAACCGGATTGGTTGCCCAGTAGAAGGCTCGTAGTCACCGGACACGCTG
251..300 TTCTTAAGGTCGGTAAGCTATTACGTCCATGGGAGATTCTCAAGGGTGCG
301..350 TTAGCGGACCCCCGTTACGTCCACGTATCTTCCGTCCAACTACCCCCTAA
351..400 TGTCATTGACATCGCCCGAGTATTTAATTTATTTGAACGGCACCAATTTA
401..405 GAGCT
Substring to search: TATT
Found at position: 153..156
Found at position: 269..272
Found at position: 371..374
Found at position: 380..383</pre>
=={{header|Factor}}==
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