The Computer Language
Benchmarks Game

k-nucleotide C# .NET Core #6 program

source code

/* The Computer Language Benchmarks Game
   http://benchmarksgame.alioth.debian.org/
 *
 * submitted by Josh Goldfoot
 * 
 */

using System;
using System.IO;
using System.Collections.Generic;
using System.Linq;
using System.Text;

public class Program
{
    public static void Main(string[] args)
    {
        PrepareLookups();
        var buffer = GetBytesForThirdSequence();
        var fragmentLengths = new[] { 1, 2, 3, 4, 6, 12, 18 };
        var dicts =
            (from fragmentLength in fragmentLengths.AsParallel()
             select CountFrequency(buffer, fragmentLength)).ToArray();
        int buflen = dicts[0].Values.Sum(x => x.V);
        WriteFrequencies(dicts[0], buflen, 1);
        WriteFrequencies(dicts[1], buflen, 2);
        WriteCount(dicts[2], "GGT");
        WriteCount(dicts[3], "GGTA");
        WriteCount(dicts[4], "GGTATT");
        WriteCount(dicts[5], "GGTATTTTAATT");
        WriteCount(dicts[6], "GGTATTTTAATTTATAGT");
    }

    private static void WriteFrequencies(Dictionary<ulong, Wrapper> freq, int buflen, int fragmentLength)
    {

        double percent = 100.0 / (buflen - fragmentLength + 1);
        foreach (var line in (from k in freq.Keys
                              orderby freq[k].V descending
                              select string.Format("{0} {1:f3}", PrintKey(k, fragmentLength),
                                (freq.ContainsKey(k) ? freq[k].V : 0) * percent)))
            Console.WriteLine(line);
        Console.WriteLine();
    }

    private static void WriteCount(Dictionary<ulong, Wrapper> dictionary, string fragment)
    {
        ulong key = 0;
        var keybytes = Encoding.ASCII.GetBytes(fragment.ToLower());
        for (int i = 0; i < keybytes.Length; i++)
        {
            key <<= 2;
            key |= tonum[keybytes[i]];
        }
        Wrapper w;
        Console.WriteLine("{0}\t{1}", 
            dictionary.TryGetValue(key, out w) ? w.V : 0, 
            fragment);
    }

    private static string PrintKey(ulong key, int fragmentLength)
    {
        char[] items = new char[fragmentLength];
        for (int i = 0; i < fragmentLength; ++i)
        {
            items[fragmentLength - i - 1] = tochar[key & 0x3];
            key >>= 2;
        }
        return new string(items);
    }

    private static Dictionary<ulong, Wrapper> CountFrequency(byte[] buffer, int fragmentLength)
    {
        var dictionary = new Dictionary<ulong, Wrapper>();
        ulong rollingKey = 0;
        ulong mask = 0;
        int cursor;
        for (cursor = 0; cursor < fragmentLength - 1; cursor++)
        {
            rollingKey <<= 2;
            rollingKey |= tonum[buffer[cursor]];
            mask = (mask << 2) + 3;
        }
        mask = (mask << 2) + 3;
        int stop = buffer.Length;
        Wrapper w;
        byte cursorByte;
        while (cursor < stop)
        {
            if ((cursorByte = buffer[cursor++]) < (byte)'a')
                cursorByte = buffer[cursor++];
            rollingKey = ((rollingKey << 2) & mask) | tonum[cursorByte];
            if (dictionary.TryGetValue(rollingKey, out w))
                w.V++;
            else
                dictionary.Add(rollingKey, new Wrapper(1));
        }
        return dictionary;
    }

    private static byte[] GetBytesForThirdSequence()
    {
        const int buffersize = 2500120;
        byte[] threebuffer = null;
        var buffer = new byte[buffersize];
        int amountRead, threebuflen, indexOfFirstByteInThreeSequence, indexOfGreaterThan, threepos, tocopy;
        amountRead = threebuflen = indexOfFirstByteInThreeSequence = indexOfGreaterThan = threepos = tocopy = 0;
        bool threeFound = false;
        var source = new BufferedStream(Console.OpenStandardInput());
        while (!threeFound && (amountRead = source.Read(buffer, 0, buffersize)) > 0)
        {
            indexOfGreaterThan = Array.LastIndexOf(buffer, (byte)'>');
            threeFound = (indexOfGreaterThan > -1 &&
                buffer[indexOfGreaterThan + 1] == (byte)'T' &&
                buffer[indexOfGreaterThan + 2] == (byte)'H');
            if (threeFound)
            {
                threepos += indexOfGreaterThan;
                threebuflen = threepos - 48;
                threebuffer = new byte[threebuflen];
                indexOfFirstByteInThreeSequence = Array.IndexOf<byte>(buffer, 10, indexOfGreaterThan) + 1;
                tocopy = amountRead - indexOfFirstByteInThreeSequence;
                if (amountRead < buffersize)
                    tocopy -= 1;
                Buffer.BlockCopy(buffer, indexOfFirstByteInThreeSequence, threebuffer, 0, tocopy);
                buffer = null;
            }
            else
                threepos += amountRead;
        }
        int toread = threebuflen - tocopy;
        source.Read(threebuffer, tocopy, toread);
        return threebuffer;
    }
    
    private static byte[] tonum = new byte[256];
    private static char[] tochar = new char[4];
    private static void PrepareLookups()
    {
        tonum['a'] = 0;
        tonum['c'] = 1;
        tonum['g'] = 2;
        tonum['t'] = 3;
        tochar[0] = 'A';
        tochar[1] = 'C';
        tochar[2] = 'G';
        tochar[3] = 'T';
    }
}

public class Wrapper
{
    public int V;
    public Wrapper(int v) { V = v; }
}
    

notes, command-line, and program output

NOTES:
64-bit Ubuntu quad core
dotnet 1.0.1 005db40cd1
"System.GC.Server": true


Sun, 16 Apr 2017 15:56:51 GMT

MAKE:
cp knucleotide.csharpcore-6.csharpcore Program.cs
cp Include/csharpcore/tmp.csproj .
cp Include/csharpcore/runtimeconfig.template.json .
mkdir obj
cp Include/csharpcore/tmp.csproj.nuget.g.props ./obj
cp Include/csharpcore/tmp.csproj.nuget.g.targets ./obj
/usr/bin/dotnet build -c Release
Microsoft (R) Build Engine version 15.1.548.43366
Copyright (C) Microsoft Corporation. All rights reserved.

  tmp -> /home/dunham/benchmarksgame_quadcore/knucleotide/tmp/bin/Release/netcoreapp1.1/tmp.dll

Build succeeded.
    0 Warning(s)
    0 Error(s)

Time Elapsed 00:00:03.72
4.19s to complete and log all make actions

COMMAND LINE:
/usr/bin/dotnet ./bin/Release/netcoreapp1.1/tmp.dll 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