source code
/* The Computer Language Benchmarks Game
https://salsa.debian.org/benchmarksgame-team/benchmarksgame/
*
* byte processing version using C# *3.0 idioms by Robert F. Tobler
*/
using System;
using System.IO;
using System.Collections.Generic;
using System.Text;
public struct ByteString : IEquatable<ByteString>
{
public byte[] Array;
public int Start;
public int Length;
public ByteString(byte[] array, int start, int length)
{
Array = array; Start = start; Length = length;
}
public ByteString(string text)
{
Start = 0; Length = text.Length;
Array = Encoding.ASCII.GetBytes(text);
}
public override int GetHashCode()
{
if (Length < 1) return 0;
int hc = Length ^ (Array[Start] << 24); if (Length < 2) return hc;
hc ^= Array[Start+Length-1] << 20; if (Length < 3) return hc;
for (int c = Length-2; c > 0; c--)
hc ^= Array[Start + c] << (c & 0xf);
return hc;
}
public bool Equals(ByteString other)
{
if (Length != other.Length) return false;
for (int i = 0; i < Length; i++)
if (Array[Start+i] != other.Array[other.Start+i]) return false;
return true;
}
public override string ToString()
{
return Encoding.ASCII.GetString(Array, Start, Length);
}
}
public static class Extensions
{
public static byte[] GetBytes(this List<string> input)
{
int count = 0;
for (int i = 0; i < input.Count; i++) count += input[i].Length;
var byteArray = new byte[count];
count = 0;
for (int i = 0; i < input.Count; i++)
{
string line = input[i];
Encoding.ASCII.GetBytes(line, 0, line.Length, byteArray, count);
count += line.Length;
}
return byteArray;
}
}
public class program {
public static void Main(string[] args) {
string line;
StreamReader source = new StreamReader(Console.OpenStandardInput());
var input = new List<string>();
while ( (line = source.ReadLine() ) != null )
if (line[0] == '>' && line.Substring(1, 5) == "THREE")
break;
while ( (line = source.ReadLine()) != null ) {
char c = line[0];
if (c == '>') break;
if (c != ';') input.Add(line.ToUpper());
}
KNucleotide kn = new KNucleotide(input.GetBytes());
input = null;
for (int f = 1; f < 3; f++) kn.WriteFrequencies(f);
foreach (var seq in
new[] { "GGT", "GGTA", "GGTATT", "GGTATTTTAATT",
"GGTATTTTAATTTATAGT"})
kn.WriteCount(seq);
}
}
public class KNucleotide {
private class Count {
public int V;
public Count(int v) { V = v; }
}
private Dictionary<ByteString, Count> frequencies
= new Dictionary<ByteString, Count>();
private byte[] sequence;
public KNucleotide(byte[] s) { sequence = s; }
public void WriteFrequencies(int length) {
GenerateFrequencies(length);
var items = new List<KeyValuePair<ByteString, Count>>(frequencies);
items.Sort(SortByFrequencyAndCode);
double percent = 100.0 / (sequence.Length - length + 1);
foreach (var item in items)
Console.WriteLine("{0} {1:f3}",
item.Key.ToString(), item.Value.V * percent);
Console.WriteLine();
}
public void WriteCount(string fragment) {
GenerateFrequencies(fragment.Length);
Count count;
if (!frequencies.TryGetValue(new ByteString(fragment), out count))
count = new Count(0);
Console.WriteLine("{0}\t{1}", count.V, fragment);
}
private void GenerateFrequencies(int length) {
frequencies.Clear();
for (int frame = 0; frame < length; frame++)
KFrequency(frame, length);
}
private void KFrequency(int frame, int k) {
int n = sequence.Length - k + 1;
for (int i = frame; i < n; i += k) {
var key = new ByteString(sequence, i, k);
Count count;
if (frequencies.TryGetValue(key, out count))
count.V++;
else
frequencies[key] = new Count(1);
}
}
int SortByFrequencyAndCode(
KeyValuePair<ByteString, Count> i0,
KeyValuePair<ByteString, Count> i1) {
int order = i1.Value.V.CompareTo(i0.Value.V);
if (order != 0) return order;
return i0.Key.ToString().CompareTo(i1.Key.ToString());
}
}
notes, command-line, and program output
NOTES:
64-bit Ubuntu quad core
.NET SDK 8.0.204
Host Version: 8.0.4
Commit: 2d7eea2529
<AllowUnsafeBlocks>true
<ServerGarbageCollection>true
<ConcurrentGarbageCollection>true
<PublishAot>false
<OptimizationPreference>Speed
<IlcInstructionSet>native
Fri, 26 Apr 2024 00:43:48 GMT
MAKE:
cp knucleotide.csharpcore-7.csharpcore Program.cs
cp Include/csharpcore/program.csproj .
mkdir obj
cp Include/csharpcore/project.assets.json ./obj
/usr/bin/dotnet build -c Release --use-current-runtime
MSBuild version 17.9.8+b34f75857 for .NET
Determining projects to restore...
Restored /home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/program.csproj (in 166 ms).
/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/Program.cs(71,14): warning CS8981: The type name 'program' only contains lower-cased ascii characters. Such names may become reserved for the language. [/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/program.csproj]
/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/Program.cs(79,25): warning CS8600: Converting null literal or possible null value to non-nullable type. [/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/program.csproj]
/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/Program.cs(83,25): warning CS8600: Converting null literal or possible null value to non-nullable type. [/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/program.csproj]
/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/Program.cs(127,68): warning CS8600: Converting null literal or possible null value to non-nullable type. [/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/program.csproj]
/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/Program.cs(143,50): warning CS8600: Converting null literal or possible null value to non-nullable type. [/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/program.csproj]
program -> /home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/bin/Release/net8.0/linux-x64/program.dll
Build succeeded.
/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/Program.cs(71,14): warning CS8981: The type name 'program' only contains lower-cased ascii characters. Such names may become reserved for the language. [/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/program.csproj]
/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/Program.cs(79,25): warning CS8600: Converting null literal or possible null value to non-nullable type. [/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/program.csproj]
/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/Program.cs(83,25): warning CS8600: Converting null literal or possible null value to non-nullable type. [/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/program.csproj]
/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/Program.cs(127,68): warning CS8600: Converting null literal or possible null value to non-nullable type. [/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/program.csproj]
/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/Program.cs(143,50): warning CS8600: Converting null literal or possible null value to non-nullable type. [/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/program.csproj]
5 Warning(s)
0 Error(s)
Time Elapsed 00:00:03.97
5.64s to complete and log all make actions
COMMAND LINE:
./bin/Release/net8.0/linux-x64/program 0 < knucleotide-input25000000.txt
PROGRAM OUTPUT:
A 30.295
T 30.151
C 19.800
G 19.754
AA 9.177
TA 9.132
AT 9.131
TT 9.091
CA 6.002
AC 6.001
AG 5.987
GA 5.984
CT 5.971
TC 5.971
GT 5.957
TG 5.956
CC 3.917
GC 3.911
CG 3.909
GG 3.902
1471758 GGT
446535 GGTA
47336 GGTATT
893 GGTATTTTAATT
893 GGTATTTTAATTTATAGT