source code
/* The Computer Language Benchmarks Game
https://salsa.debian.org/benchmarksgame-team/benchmarksgame/
*
* byte processing, C# 3.0 idioms, frame level paralellism by Robert F. Tobler
*/
using System;
using System.IO;
using System.Collections.Generic;
using System.Linq;
using System.Text;
using System.Threading;
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()
{
int hc = 0;
for (int i = 0; i < Length; i++)
hc = hc * 31 + Array[Start + i];
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> lines)
{
int count = lines.Aggregate(0, (cnt, str) => cnt + str.Length);
var array = new byte[count];
lines.Aggregate(0, (pos, str) => {
Encoding.ASCII.GetBytes(str, 0, str.Length, array, pos);
return pos + str. Length;
});
return array;
}
}
public class Program
{
public static int TaskCount;
public static int Current = -1;
public static KNucleotide[] kna;
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());
}
var lengths = new [] { 1, 2, 3, 4, 6, 12, 18 };
TaskCount = lengths.Aggregate(0, (cnt, len) => cnt + len);
kna = new KNucleotide[TaskCount];
var bytes = input.GetBytes();
lengths.Aggregate(0, (cnt, len) =>
{
for (int i = 0; i < len; i++)
kna[cnt + i] = new KNucleotide(bytes, len, i);
return cnt + len;
});
var threads = new Thread[Environment.ProcessorCount];
for (int i = 0; i < threads.Length; i++)
(threads[i] = new Thread(CountFrequencies)).Start();
foreach (var t in threads)
t.Join();
var seqs = new[] { null, null,
"GGT", "GGTA", "GGTATT", "GGTATTTTAATT",
"GGTATTTTAATTTATAGT"};
int index = 0;
lengths.Aggregate(0, (cnt, len) =>
{
if (len < 3)
{
for (int i = 1; i < len; i++)
kna[cnt].AddFrequencies(kna[cnt+i]);
kna[cnt].WriteFrequencies();
}
else
{
var fragment = seqs[index];
int freq = 0;
for (int i = 0; i < len; i++)
freq += kna[cnt + i].GetCount(fragment);
Console.WriteLine("{0}\t{1}", freq, fragment);
}
index++;
return cnt + len;
});
}
static void CountFrequencies()
{
int index;
while ((index = Interlocked.Increment(ref Current)) < TaskCount)
kna[index].KFrequency();
}
}
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;
int length;
int frame;
public KNucleotide(byte[] s, int l, int f)
{
sequence = s; length = l; frame = f;
}
public void AddFrequencies(KNucleotide other)
{
foreach(var kvp in other.frequencies)
{
Count count;
if (frequencies.TryGetValue(kvp.Key, out count))
count.V += kvp.Value.V;
else
frequencies[kvp.Key] = kvp.Value;
}
}
public void WriteFrequencies() {
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 int GetCount(string fragment) {
Count count;
if (!frequencies.TryGetValue(new ByteString(fragment), out count))
count = new Count(0);
return count.V;
}
public void KFrequency() {
int n = sequence.Length - length + 1;
for (int i = frame; i < n; i += length) {
var key = new ByteString(sequence, i, length);
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 00:48:57 GMT
MAKE:
cp knucleotide.csharpcore-4.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 178 ms).
/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/Program.cs(166,54): 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(185,68): 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(195,50): 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(78,25): 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(82,25): 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(126,55): warning CS8604: Possible null reference argument for parameter 'fragment' in 'int KNucleotide.GetCount(string fragment)'. [/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/program.csproj]
/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/Program.cs(71,33): warning CS8618: Non-nullable field 'kna' must contain a non-null value when exiting constructor. Consider declaring the field as nullable. [/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(166,54): 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(185,68): 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(195,50): 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(78,25): 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(82,25): 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(126,55): warning CS8604: Possible null reference argument for parameter 'fragment' in 'int KNucleotide.GetCount(string fragment)'. [/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/program.csproj]
/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/Program.cs(71,33): warning CS8618: Non-nullable field 'kna' must contain a non-null value when exiting constructor. Consider declaring the field as nullable. [/home/dunham/all-benchmarksgame/benchmarksgame_i53330/knucleotide/tmp/program.csproj]
7 Warning(s)
0 Error(s)
Time Elapsed 00:00:03.90
5.53s 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