public void ColumnsSetters()
{
// Arrange
var rg = new RegionGenerator
{
ChrColumn = 2,
LeftColumn = 2,
RightColumn = 9,
StrandColumn = -1,
SourceColumn = 2,
FeatureColumn = -1
};
rg.StrandColumn = 0;
rg.StrandColumn = 19;
rg.FeatureColumn = 8;
using (var file = new TempFileCreator(rg))
{
// Act
var parsedGTF = Features.ParseGTF(file.TempFilePath, rg);
var parsedFeature = parsedGTF.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals[0];
// Assert
Assert.True(parsedFeature.CompareTo(rg.GFeature) == 0);
}
}
public void ColumnsShuffle(
byte chrColumn, sbyte sourceColumn, sbyte featureColumn, byte leftColumn, sbyte rightColumn,
sbyte scoreColumn, sbyte strandColumn, sbyte frameColumn, sbyte attributeColumn)
{
// Arrange
var rg = new RegionGenerator()
{
ChrColumn = chrColumn,
SourceColumn = sourceColumn,
FeatureColumn = featureColumn,
LeftColumn = leftColumn,
RightColumn = rightColumn,
ScoreColumn = scoreColumn,
StrandColumn = strandColumn,
FrameColumn = frameColumn,
AttributeColumn = attributeColumn
};
using (var file = new TempFileCreator(rg))
{
// Act
var parsedGTF = Features.ParseGTF(file.TempFilePath, rg);
var parsedFeature = parsedGTF.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 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 FeatureCount()
{
// Arrange
var rg = new RegionGenerator {
Feature = "feature"
};
int featureCount = 5;
using (var file = new TempFileCreator(rg, featuresCount: featureCount))
{
// Act
var parsedGTF = ParseGTF(file.TempFilePath, rg);
// Assert
Assert.True(parsedGTF.DeterminedFeatures[rg.Feature] == featureCount);
}
}
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);
}
}
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 MultiFeatureFile()
{
// Arrange
var rg = new RegionGenerator
{
StrandColumn = 12
};
using (var file = new TempFileCreator(rg, featuresCount: 10, headerLineCount: 2))
{
// Act
var parsedData = ParseGTF(file.TempFilePath, rg);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.Count == 10);
}
}
public void TestInvalidFeatureColumn()
{
// Arrange
var rg = new RegionGenerator
{
// a column number which is more than the number of columns written to the test file.
FeatureColumn = 10
};
using (var file = new TempFileCreator("chr1\tDi4\t.\t10\t20\t100.0\t*\t0\tatt1=1;att2=v2"))
{
// Act
var parsedGTF = Features.ParseGTF(file.TempFilePath, rg);
// Assert
Assert.False(parsedGTF.Chromosomes.ContainsKey("chr1"));
}
}
public void TestFrameColumn(sbyte frameColumn, string frame)
{
// Arrange
var rg = new RegionGenerator
{
Frame = frame,
FrameColumn = frameColumn
};
using (var file = new TempFileCreator(rg))
{
// Act
var parsedGTF = Features.ParseGTF(file.TempFilePath, rg);
var parsedFeature = parsedGTF.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.ToList()[0];
// Assert
Assert.True(parsedFeature.Frame == frame);
}
}
public void TestScoreColumn(sbyte scoreColumn, double score)
{
// Arrange
var rg = new RegionGenerator
{
Score = score,
ScoreColumn = scoreColumn
};
using (var file = new TempFileCreator(rg))
{
// Act
var parsedGTF = Features.ParseGTF(file.TempFilePath, rg);
var parsedFeature = parsedGTF.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals[0];
// Assert
Assert.True(double.IsNaN(score) ? double.IsNaN(parsedFeature.Score) : parsedFeature.Score == score);
}
}
public void TestAttributeColumn(sbyte attributeColumn, string attribute)
{
// Arrange
var rg = new RegionGenerator
{
Attribute = attribute,
AttributeColumn = attributeColumn
};
using (var file = new TempFileCreator(rg))
{
// Act
var parsedGTF = Features.ParseGTF(file.TempFilePath, rg);
var parsedFeature = parsedGTF.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals[0];
// Assert
Assert.True(parsedFeature.Attribute == attribute);
}
}
public TempFileCreator(RegionGenerator columns, int headerLineCount = 0, int featuresCount = 1)
{
TempFilePath = Path.GetTempPath() + Guid.NewGuid().ToString() + ".gtf";
FileStream stream = File.Create(TempFilePath);
using (StreamWriter writer = new StreamWriter(stream))
{
while (headerLineCount-- > 0)
{
writer.WriteLine(columns.GetSampleHeader());
}
while (featuresCount-- > 0)
{
writer.WriteLine(columns.GetSampleLine());
if (featuresCount > 0)
{
columns.Left = columns.Right + 10;
columns.Right = columns.Right + 20;
}
}
}
}
internal static Gtf <GeneralFeature> ParseGTF(string filePath, RegionGenerator rg)
{
var parser = new GtfParser(rg.Columns);
return(parser.Parse(filePath));
}