public static void Analyze(string fileName)
{
var letterCount = KnownLetters.Length;
var singleLetterFrequency = new CappedFrequencyCounter <char>(letterCount);
var doubleLetterFrequency = new CappedFrequencyCounter <string>(letterCount * letterCount);
var threeLetterFrequency = new CappedFrequencyCounter <string>(letterCount * letterCount * letterCount);
var fiveLetterFrequency = new CappedFrequencyCounter <string>(letterCount * letterCount * letterCount * letterCount * letterCount);
var tenLetterFrequency = new CappedFrequencyCounter <string>(100000);
var letterBuffer = new CircularBuffer <char>(10);
var baseIndex = 0uL;
var lineIdx = 0;
using (var streamReader = new StreamReader(fileName))
{
string line;
while ((line = streamReader.ReadLine()) != null)
{
lineIdx++;
if (line.StartsWith(">"))
{
continue;
}
if (lineIdx % (1000 * 1000) == 0)
{
Console.WriteLine($"Line {lineIdx}, base {baseIndex}");
}
foreach (var c in line)
{
if (!KnownLetters.Contains(c))
{
throw new Exception($"Unknown base {c}");
}
baseIndex++;
letterBuffer.Put(c);
singleLetterFrequency.Add(c);
if (baseIndex > 1)
{
var doubleLetter = new string(letterBuffer.Take(2).ToArray());
doubleLetterFrequency.Add(doubleLetter);
}
if (baseIndex > 2)
{
var threeLetter = new string(letterBuffer.Take(3).ToArray());
threeLetterFrequency.Add(threeLetter);
}
if (baseIndex > 4)
{
var fiveLetter = new string(letterBuffer.Take(5).ToArray());
fiveLetterFrequency.Add(fiveLetter);
}
if (baseIndex > 9)
{
var tenLetter = new string(letterBuffer.Take(10).ToArray());
tenLetterFrequency.Add(tenLetter);
}
}
if (lineIdx > 55 * 1000 * 1000)
{
break;
}
}
}
File.WriteAllText("nucleotide_statistics.txt", ""
+ singleLetterFrequency.Counter.OrderByDescending(kvp => kvp.Value).Select(kvp => kvp.Key + ": " + kvp.Value).Aggregate((a, b) => a + Environment.NewLine + b) + Environment.NewLine
+ "--------------------" + Environment.NewLine
+ doubleLetterFrequency.Counter.OrderByDescending(kvp => kvp.Value).Select(kvp => kvp.Key + ": " + kvp.Value).Aggregate((a, b) => a + Environment.NewLine + b) + Environment.NewLine
+ "--------------------" + Environment.NewLine
+ threeLetterFrequency.Counter.OrderByDescending(kvp => kvp.Value).Select(kvp => kvp.Key + ": " + kvp.Value).Aggregate((a, b) => a + Environment.NewLine + b) + Environment.NewLine
+ "--------------------" + Environment.NewLine
+ fiveLetterFrequency.Counter.OrderByDescending(kvp => kvp.Value).Select(kvp => kvp.Key + ": " + kvp.Value).Aggregate((a, b) => a + Environment.NewLine + b) + Environment.NewLine
+ "--------------------" + Environment.NewLine
+ tenLetterFrequency.Counter.OrderByDescending(kvp => kvp.Value).Select(kvp => kvp.Key + ": " + kvp.Value).Aggregate((a, b) => a + Environment.NewLine + b) + Environment.NewLine);
}
public FixedLengthSequenceFrequencyCounter(int sequenceLength, int combinationLimit)
{
this.SequenceLength = sequenceLength;
circularBuffer = new CircularBuffer <char>(sequenceLength);
FrequencyCounter = new CappedFrequencyCounter <string>(combinationLimit);
}