public void FailReadRight()
{
// Arrange
using (var file = new TempFileCreator("chr1\tSource\tFeature\t10\t20V\t100.0\t*\t0\tatt1=1;att2=v2"))
{
// ACt
var parser = new GtfParser();
var parsedData = parser.Parse(file.TempFilePath);
// Assert
Assert.False(parsedData.Chromosomes.ContainsKey("chr1"));
}
}
public void FullySetArguments()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new GtfParser(rg.Columns);
var parsedFeature = parser.Parse(file.TempFilePath).Chromosomes[rg.Chr].Strands[rg.Strand].Intervals[0];
// Assert
Assert.True(parsedFeature.CompareTo(rg.GFeature) == 0);
}
}
public void ReadStrand()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new GtfParser();
var parsedData = parser.Parse(file.TempFilePath);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands.ContainsKey(rg.Strand));
}
}
public void AssignHashKey()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new GtfParser();
var parsedData = parser.Parse(file.TempFilePath);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.ToList()[0].GetHashCode() != 0);
}
}
public void TestDefaultColumnOrder()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new GtfParser();
var parsedFeature = parser.Parse(file.TempFilePath).Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.ToList()[0];
// Assert
Assert.True(parsedFeature.CompareTo(rg.GFeature) == 0);
}
}
public void AvoidHeader(int headerCount, byte readOffset)
{
// Arrange
using (var file = new TempFileCreator(new RegionGenerator(), headerLineCount: headerCount))
{
// Act
var parser = new GtfParser()
{
ReadOffset = readOffset
};
var parsedData = parser.Parse(file.TempFilePath);
// Assert
Assert.True(parsedData.Chromosomes.Count == 1);
}
}
public void ReadLeft()
{
// Arrange
var rg = new RegionGenerator {
Left = 10
};
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new GtfParser();
var parsedData = parser.Parse(file.TempFilePath);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.ToList()[0].Left == rg.Left);
}
}
public void FailReadChr(string chr)
{
// Arrange
var rg = new RegionGenerator {
Chr = "chr1"
};
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new GtfParser();
var parsedData = parser.Parse(file.TempFilePath);
// Assert
Assert.False(parsedData.Chromosomes.ContainsKey(chr));
}
}
public void ReadAttribute()
{
// Arrange
var rg = new RegionGenerator {
Attribute = "att1=at1;att2=at2;att3=3"
};
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new GtfParser();
var parsedData = parser.Parse(file.TempFilePath);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.ToList()[0].Attribute == rg.Attribute);
}
}
public void ReadScore()
{
// Arrange
var rg = new RegionGenerator {
Score = 123.456
};
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new GtfParser();
var parsedData = parser.Parse(file.TempFilePath);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals[0].Score == rg.Score);
}
}
internal static Gtf <GeneralFeature> ParseGTF(string filePath, RegionGenerator rg)
{
var parser = new GtfParser(rg.Columns);
return(parser.Parse(filePath));
}