public void ReadTwoIntervalsWithExactSameInfo()
{
// Arrange
var peak = "chr1\t10\t20\tGeUtilities_00\t0.01";
using var file = new TempFileCreator(new string[] { peak, peak });
// Act
var parser = new BedParser();
var parsedBED = parser.Parse(file.Path);
// Assert
Assert.True(parsedBED.IntervalsCount == 2);
}
public void CanTellIfStrandContainsAnInterval()
{
// Arrange
using (var file = new TempFileCreator())
{
// Act
var parser = new BedParser();
var parsedBED = parser.Parse(file.Path);
var interval = parsedBED.Chromosomes["chr1"].Strands['.'].Intervals.ToList()[0];
// Assert
Assert.True(parsedBED.Chromosomes["chr1"].Strands['.'].Contains(interval));
}
}
protected virtual void Dispose(bool disposing)
{
if (!this.disposed)
{
if (disposing)
{
this.fileCreator?.Dispose();
}
this.fileCreator = null;
this.disposed = true;
}
}
public void TestFilePath()
{
// Arrange
string peak = "chr1\t10\t20\tName\t100.0";
using (var file = new TempFileCreator(peak))
{
// Act
var parser = new BedParser();
var parsedBED = parser.Parse(file.Path);
// Assert
Assert.True(parsedBED.FilePath == Path.GetFullPath(file.Path));
}
}
public void CanGetAnIntervalFromStrand()
{
// Arrange
using (var file = new TempFileCreator())
{
// Act
var parser = new BedParser();
var parsedBED = parser.Parse(file.Path);
var expected = parsedBED.Chromosomes["chr1"].Strands['.'].Intervals.ToList()[0];
// Assert
GeUtilities.Intervals.Model.Peak i;
Assert.True(parsedBED.Chromosomes["chr1"].Strands['.'].TryGet(expected.GetHashCode(), out i));
Assert.Equal(expected, i);
}
}
public void TestAssembly(Assemblies assembly)
{
// Arrange
string peak = "chr1\t10\t20\tName\t100.0";
using (var file = new TempFileCreator(peak))
{
// Act
var parser = new BedParser()
{
Assembly = assembly
};
var parsedBED = parser.Parse(file.Path);
// Assert
Assert.True(parsedBED.Assembly == assembly);
}
}
public void TestPValueHighestInParsedDataPerChr()
{
string[] peaks = new string[]
{
"chr1\t10\t20\tGeUtilities_00\t0.1",
"chr1\t30\t40\tGeUtilities_01\t0.01",
"chr1\t50\t60\tGeUtilities_02\t0.001",
"chr2\t10\t20\tGeUtilities_00\t0.2",
};
using (var file = new TempFileCreator(peaks))
{
var parser = new BedParser()
{
PValueFormat = PValueFormats.SameAsInput
};
var parsedData = parser.Parse(file.Path);
Assert.True(parsedData.Chromosomes["chr1"].Statistics.PValueHighest == 0.1);
}
}
