The Computer Language
Benchmarks Game

k-nucleotide C# Mono LLVM #7 program

source code

/* The Computer Language Benchmarks Game
   http://benchmarksgame.alioth.debian.org/
 *
 * byte processing, C# 3.0 idioms, frame level paralellism by Robert F. Tobler
 * modified by Rene Koeldorfer
 */

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


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 KNucleotideNode {
      public int V;
      public int KeyLength;
      public KNucleotideNode(int v,int keyLength) { V = v;KeyLength=keyLength; }
   }
   private static byte[] tonum=new byte[256];
   private static char[] tochar=new char[4];

   static KNucleotide()
   {
      tonum['A'] = 0;
      tonum['C'] = 1;
      tonum['T'] = 2;
      tonum['G'] = 3;
      tochar[0] = 'A';
      tochar[1] = 'C';
      tochar[2] = 'T';
      tochar[3] = 'G';
   }

   private static ulong CreateKey(byte[] s,int keyStart,int keyLength)
   {
      ulong key = 0;
      for(int i = 0; i < keyLength; i++)
      {
         key <<= 2;
         key |= tonum[s[keyStart+i]];
      }
      return key;
   }

   private static string PrintKey(ulong key,int keyLenght)
   {

      char[] items = new char[keyLenght];
      for(int i = 0; i < keyLenght; ++i)
      {
         items[keyLenght-i-1]=tochar[key & 0x3];
         key >>= 2;
      }
      return new string(items);
   }

   private ulong CreateKey(byte[] s,int start)
   {
      return CreateKey (s, start, length);
   }

   private static ulong CreateKey(string keyString)
   {
      byte[] byteArray = System.Text.Encoding.ASCII.GetBytes (keyString);
      return CreateKey (byteArray, 0, keyString.Length);
   }


   private Dictionary<ulong, KNucleotideNode> frequencies
   = new Dictionary<ulong, KNucleotideNode>();
   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)            
      {
         KNucleotideNode kNucleotideNode;
         if (frequencies.TryGetValue(kvp.Key, out kNucleotideNode))
            kNucleotideNode.V += kvp.Value.V;
         else
            frequencies[kvp.Key] = kvp.Value;
      }
   }

   public void WriteFrequencies() {
      var items = new List<KeyValuePair<ulong, KNucleotideNode>>(frequencies);
      items.Sort(SortByFrequencyAndCode);    
      double percent = 100.0 / (sequence.Length - length + 1);
      foreach (var item in items)
         Console.WriteLine("{0} {1:f3}",
            PrintKey(item.Key,item.Value.KeyLength), item.Value.V * percent);
      Console.WriteLine();
   }

   public int GetCount(string fragment) {
      KNucleotideNode kNucleotideNode;
      ulong key = CreateKey (fragment);
      if (!frequencies.TryGetValue(key, out kNucleotideNode))
         kNucleotideNode = new KNucleotideNode(0,0);
      return kNucleotideNode.V;
   }

   public void KFrequency() {
      int n = sequence.Length - length + 1;
      for (int i = frame; i < n; i += length) {
         var key = CreateKey(sequence, i, length);
         KNucleotideNode kNucleotideNode;
         if (frequencies.TryGetValue(key, out kNucleotideNode))
            kNucleotideNode.V++;
         else
            frequencies[key] = new KNucleotideNode(1,length);
      }
   }

   int SortByFrequencyAndCode(
      KeyValuePair<ulong, KNucleotideNode> i0,
      KeyValuePair<ulong, KNucleotideNode> i1) {
      int order = i1.Value.V.CompareTo(i0.Value.V);
      if (order != 0) return order;
      return i0.Key.CompareTo(i1.Key);
   }
}
    

notes, command-line, and program output

NOTES:
32-bit Ubuntu one core
Mono JIT compiler version 4.5.1 (master/3e844dd Fri May  6 19:24:07 PDT 2016)
	LLVM:          yes(3.6.0svn-mono-master/9f79399)
	GC:            sgen



Tue, 28 Jun 2016 19:04:31 GMT

MAKE:
mv knucleotide.csharpllvm-7.csharpllvm knucleotide.csharpllvm-7.cs
/usr/local/bin/mcs -unsafe+ -optimize+ -platform:x86 -out:knucleotide.csharpllvm-7.csharpllvm_run knucleotide.csharpllvm-7.cs
rm knucleotide.csharpllvm-7.cs
0.31s to complete and log all make actions

COMMAND LINE:
/usr/local/bin/mono --llvm --gc=sgen knucleotide.csharpllvm-7.csharpllvm_run 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