public void CreateStatsWithMixedcaseLetterSequence()
{
ISequence sequence = new Sequence(Alphabets.DNA, "aAaAaAaA");
SequenceStatistics stats = new SequenceStatistics(sequence);
Assert.AreEqual(8, stats.GetCount('A'));
Assert.AreEqual(8, stats.GetCount(65));
Assert.AreEqual(8, stats.GetCount('a'));
Assert.AreEqual(1.0, stats.GetFraction('A'));
Assert.AreEqual(1.0, stats.GetFraction(65));
Assert.AreEqual(1.0, stats.GetFraction('a'));
}
public void CreateSimpleStatsWithSingleLetterSequence()
{
ISequence sequence = new Sequence(Alphabets.DNA, "A");
SequenceStatistics stats = new SequenceStatistics(sequence);
Assert.AreEqual(1, stats.GetCount('A'));
Assert.AreEqual(1, stats.GetCount(65));
Assert.AreEqual(0, stats.GetCount('C'));
Assert.AreEqual(0, stats.GetCount('G'));
Assert.AreEqual(0, stats.GetCount('T'));
Assert.AreEqual(1.0, stats.GetFraction('A'));
Assert.AreEqual(1.0, stats.GetFraction(65));
}
public void CreateSimpleStatsWithSingleLetterSequence()
{
ISequence sequence = new Sequence(Alphabets.DNA, "A");
SequenceStatistics stats = new SequenceStatistics(sequence);
Assert.AreEqual(1, stats.GetCount('A'));
Assert.AreEqual(1, stats.GetCount(65));
Assert.AreEqual(0, stats.GetCount('C'));
Assert.AreEqual(0, stats.GetCount('G'));
Assert.AreEqual(0, stats.GetCount('T'));
Assert.AreEqual(1.0, stats.GetFraction('A'));
Assert.AreEqual(1.0, stats.GetFraction(65));
}
static void DumpStatsForOneSequence()
{
ISequence oneSequence = null;
var parser = SequenceParsers.FindParserByFileName(Filename);
if (parser != null)
{
oneSequence = parser.Parse().First();
parser.Close();
}
if (oneSequence == null)
{
Console.WriteLine("Could not load sequence.");
return;
}
SequenceStatistics stats =
new SequenceStatistics(oneSequence);
foreach (var symbol in oneSequence.Alphabet)
{
Console.WriteLine("{0} = Count={1}, Fraction={2}",
(char)symbol, stats.GetCount(symbol),
stats.GetFraction(symbol));
}
}
static void Main(string[] args)
{
var parser = SequenceParsers.FindParserByFileName(Filename);
if (parser == null)
{
Console.WriteLine("No parser found.");
return;
}
List <ISequence> allSequences = parser
.Parse()
.ToList();
IAlphabet alphabet = allSequences[0].Alphabet;
long totalColums = allSequences.Min(s => s.Count);
//byte[] data = new byte[allSequences.Count];
for (int column = 0; column < totalColums; column++)
{
// for (int row = 0; row < allSequences.Count; row++)
// data[row] = allSequences[row][column];
//ISequence newSequence = new Sequence(alphabet, data);
ISequence newSequence = new Sequence(AmbiguousRnaAlphabet.Instance,
allSequences
.Select(s => s[column]).ToArray());
SequenceStatistics stats =
new SequenceStatistics(newSequence);
var TopCount =
alphabet
.Where(symbol => !alphabet.CheckIsGap(symbol))
.Select(symbol =>
new
{
Symbol = (char)symbol,
Count = stats.GetCount(symbol),
Frequency = stats.GetFraction(symbol)
})
.Where(tc => tc.Count > 0)
.OrderByDescending(c => c.Count)
.FirstOrDefault();
if (TopCount != null)
{
Console.WriteLine("{0}: {1} = {2} of {3}",
column, TopCount.Symbol, TopCount.Count, totalColums);
}
}
}
public void CreateStatsWithSeveralMixedcaseLetterSequence()
{
ISequence sequence = new Sequence(Alphabets.DNA, "a-c-g-t-A-C-G-T-");
SequenceStatistics stats = new SequenceStatistics(sequence);
Assert.AreEqual(2, stats.GetCount('A'));
Assert.AreEqual(2, stats.GetCount('a'));
Assert.AreEqual(2, stats.GetCount('C'));
Assert.AreEqual(2, stats.GetCount('c'));
Assert.AreEqual(2, stats.GetCount('G'));
Assert.AreEqual(2, stats.GetCount('g'));
Assert.AreEqual(2, stats.GetCount('T'));
Assert.AreEqual(2, stats.GetCount('t'));
Assert.AreEqual(8, stats.GetCount('-'));
Assert.AreEqual(2.0 / 16.0, stats.GetFraction('A'));
Assert.AreEqual(2.0 / 16.0, stats.GetFraction('C'));
Assert.AreEqual(2.0 / 16.0, stats.GetFraction('G'));
Assert.AreEqual(2.0 / 16.0, stats.GetFraction('T'));
Assert.AreEqual(.5, stats.GetFraction('-'));
Assert.AreEqual(.5, stats.GetFraction(45));
}
public void CreateStatsWithMixedcaseLetterSequence()
{
ISequence sequence = new Sequence(Alphabets.DNA, "aAaAaAaA");
SequenceStatistics stats = new SequenceStatistics(sequence);
Assert.AreEqual(8, stats.GetCount('A'));
Assert.AreEqual(8, stats.GetCount(65));
Assert.AreEqual(8, stats.GetCount('a'));
Assert.AreEqual(1.0, stats.GetFraction('A'));
Assert.AreEqual(1.0, stats.GetFraction(65));
Assert.AreEqual(1.0, stats.GetFraction('a'));
}
public void CreateStatsWithSeveralMixedcaseLetterSequence()
{
ISequence sequence = new Sequence(Alphabets.DNA, "a-c-g-t-A-C-G-T-");
SequenceStatistics stats = new SequenceStatistics(sequence);
Assert.AreEqual(2, stats.GetCount('A'));
Assert.AreEqual(2, stats.GetCount('a'));
Assert.AreEqual(2, stats.GetCount('C'));
Assert.AreEqual(2, stats.GetCount('c'));
Assert.AreEqual(2, stats.GetCount('G'));
Assert.AreEqual(2, stats.GetCount('g'));
Assert.AreEqual(2, stats.GetCount('T'));
Assert.AreEqual(2, stats.GetCount('t'));
Assert.AreEqual(8, stats.GetCount('-'));
Assert.AreEqual(2.0 / 16.0, stats.GetFraction('A'));
Assert.AreEqual(2.0 / 16.0, stats.GetFraction('C'));
Assert.AreEqual(2.0 / 16.0, stats.GetFraction('G'));
Assert.AreEqual(2.0 / 16.0, stats.GetFraction('T'));
Assert.AreEqual(.5, stats.GetFraction('-'));
Assert.AreEqual(.5, stats.GetFraction(45));
}