public void TestIsRepeat()
{
// mononucleotide repeats
Assert.True(OverlapEvaluator.IsRepeat("AAAAAAA"));
Assert.False(OverlapEvaluator.IsRepeat("TAAAAA"));
Assert.False(OverlapEvaluator.IsRepeat("AAATAA"));
Assert.False(OverlapEvaluator.IsRepeat("AAAAAT"));
// dinucleotide repeats
Assert.True(OverlapEvaluator.IsRepeat("ATATAT"));
Assert.True(OverlapEvaluator.IsRepeat("ATATATA"));
Assert.False(OverlapEvaluator.IsRepeat("AATATATA"));
Assert.False(OverlapEvaluator.IsRepeat("ATATAATA"));
// trinucleotide repeats
Assert.True(OverlapEvaluator.IsRepeat("ATGATGATG")); // 3x ATG
Assert.True(OverlapEvaluator.IsRepeat("ATGATGATGA")); // 3x ATG + A
Assert.True(OverlapEvaluator.IsRepeat("ATGATGATGAT")); // 3x ATG + AT
Assert.False(OverlapEvaluator.IsRepeat("ATGATGATGAG")); // 3x ATG + AG
Assert.False(OverlapEvaluator.IsRepeat("ATGATGATGTG")); // 3x ATG + TG
Assert.True(OverlapEvaluator.IsRepeat("AA"));
Assert.False(OverlapEvaluator.IsRepeat("ATC"));
Assert.False(OverlapEvaluator.IsRepeat("AT"));
Assert.False(OverlapEvaluator.IsRepeat("A"));
Assert.True(OverlapEvaluator.IsRepeat("ATA"));
}
public void TestSlidingWindow()
{
// Short overlap, min windowsize
var units = OverlapEvaluator.SlideSequence("ATA", 1); // Will survey 3-1 = Up to index 2 positions to get [A,T,A] = [A,T]
Assert.Equal(2, units.Count());
// Short overlap, max windowsize
var units2 = OverlapEvaluator.SlideSequence("ATAG", 3); // Will survey 4-3 = Up to index 1 positions to get [ATA, TAG]
Assert.Equal(2, units2.Count());
// Long overlap, min windowsize
var units3 = OverlapEvaluator.SlideSequence("ATTTACGCAGTAGACAGATAAAAA", 1); // [A,T,T] = [A,T]
Assert.Equal(2, units3.Count());
// Long overlap, max windowsize
var units4 = OverlapEvaluator.SlideSequence("ATGATGATGATGATGATGATGATG", 3); // [ATG,TGA,GAT]
Assert.Equal(3, units4.Count());
// Windowsize above maximum allowed
Assert.Throws <ArgumentException>(() => OverlapEvaluator.SlideSequence("ATGATGATGATGATGATGATGATG", 4));
}
public void TestIsRepeat()
{
// mononucleotide repeats
Assert.True(OverlapEvaluator.IsRepeat("AAAAAAA"));
Assert.False(OverlapEvaluator.IsRepeat("TAAAAA"));
Assert.False(OverlapEvaluator.IsRepeat("AAATAA"));
Assert.False(OverlapEvaluator.IsRepeat("AAAAAT"));
// dinucleotide repeats
Assert.True(OverlapEvaluator.IsRepeat("ATATAT"));
Assert.True(OverlapEvaluator.IsRepeat("ATATATA"));
Assert.False(OverlapEvaluator.IsRepeat("AATATATA"));
Assert.False(OverlapEvaluator.IsRepeat("ATATAATA"));
// trinucleotide repeats
Assert.True(OverlapEvaluator.IsRepeat("ATGATGATG")); // 3x ATG
Assert.True(OverlapEvaluator.IsRepeat("ATGATGATGA")); // 3x ATG + A
Assert.True(OverlapEvaluator.IsRepeat("ATGATGATGAT")); // 3x ATG + AT
Assert.False(OverlapEvaluator.IsRepeat("ATGATGATGAG")); // 3x ATG + AG
Assert.False(OverlapEvaluator.IsRepeat("ATGATGATGTG")); // 3x ATG + TG
Assert.True(OverlapEvaluator.IsRepeat("TGATGATGATG")); // 3x ATG, starts with end of unit
Assert.True(OverlapEvaluator.IsRepeat("GATGATGATG")); // 3x ATG, starts with end of unit
Assert.True(OverlapEvaluator.IsRepeat("GATGATGATGA")); // 3x ATG, partials on either side
Assert.True(OverlapEvaluator.IsRepeat("AA"));
Assert.False(OverlapEvaluator.IsRepeat("ATC"));
Assert.False(OverlapEvaluator.IsRepeat("AT"));
Assert.False(OverlapEvaluator.IsRepeat("A"));
Assert.True(OverlapEvaluator.IsRepeat("ATA"));
Assert.True(OverlapEvaluator.IsRepeat("ATAT"));
Assert.False(OverlapEvaluator.IsRepeat("ATGCAATGCA")); // Unit too long
}
