public void ColumnsShuffle(byte chrColumn, byte leftColumn, sbyte rightColumn, byte nameColumn, byte valueColumn)
{
// Arrange
var rg = new RegionGenerator
{
ChrColumn = chrColumn,
LeftColumn = leftColumn,
RightColumn = rightColumn,
NameColumn = nameColumn,
ValueColumn = valueColumn
};
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new BedParser(
new BedColumns()
{
Chr = chrColumn,
Left = leftColumn,
Right = rightColumn,
Name = nameColumn,
Value = valueColumn
});
var parsedPeak = parser.Parse(file.Path).Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.ToList()[0];
// Assert
Assert.True(parsedPeak.CompareTo(rg.Peak) == 0);
}
}
public void ReadStrand()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg))
{
// ACt
var parser = new BedParser();
var parsedData = parser.Parse(file.Path);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands.ContainsKey(rg.Strand));
}
}
public void FullySetArguments()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new BedParser(rg.Columns);
var parsedPeak = parser.Parse(file.Path).Chromosomes[rg.Chr].Strands[rg.Strand].Intervals[0];
// Assert
Assert.True(parsedPeak.CompareTo(rg.Peak) == 0);
}
}
public void ReadValue()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new BedParser();
var parsedData = parser.Parse(file.Path);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals[0].Value == rg.Value);
}
}
public void AssignHashKey()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new BedParser();
var parsedData = parser.Parse(file.Path);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals[0].GetHashCode() != 0);
}
}
public void DefaultColumnsOrder()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator())
{
// Act
var parser = new BedParser();
var parsedPeak = parser.Parse(file.Path).Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.ToList()[0];
// Assert
Assert.True(parsedPeak.CompareTo(rg.Peak) == 0);
}
}
public void BEDWithAllOptionalColumnsAndSomeExtraColumns()
{
// Arrange
var rg = new RegionGenerator {
SummitColumn = 10, StrandColumn = 11
};
using (var file = new TempFileCreator(rg, headerLineCount: 2, peaksCount: 10))
{
// Act
var parser = new BedParser();
var parsedData = parser.Parse(file.Path);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.Count == 10);
}
}
public void ReadNoPeak()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg, peaksCount: 4))
{
// Act
var parser = new BedParser()
{
MaxLinesToRead = 0
};
var parsedData = parser.Parse(file.Path);
// Assert
Assert.True(parsedData.Chromosomes.Count == 0);
}
}
public void MaxLinesToRead(int numberOfPeaksToWrite, uint numberOfPeaksToRead)
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg, peaksCount: numberOfPeaksToWrite))
{
// Act
var parser = new BedParser()
{
MaxLinesToRead = numberOfPeaksToRead
};
var parsedData = parser.Parse(file.Path);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.Count == Math.Min(numberOfPeaksToWrite, numberOfPeaksToRead));
}
}
public void TestStrand(sbyte strandColumn, char strand)
{
// Arrange
var rg = new RegionGenerator
{
Strand = strand,
StrandColumn = strandColumn
};
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new BedParser(rg.Columns);
// Assert
Assert.True(parser.Parse(file.Path).Chromosomes[rg.Chr].Strands.ContainsKey(strand));
}
}
public void ThrowExceptionForInvalidCultureInfo()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg))
{
// Act
var exception = Assert.Throws <ArgumentOutOfRangeException>(
() => new BedParser
{
Culture = "invalid_culture"
});
// Assert
Assert.False(string.IsNullOrEmpty(exception.Message));
Assert.Contains("Invalid culture info", exception.Message);
}
}
public void TestSummit(sbyte summitColumn, int summit)
{
// Arrange
var rg = new RegionGenerator {
SummitColumn = summitColumn
};
rg.Summit = summit == -1 ? rg.Left + ((rg.Right - rg.Left) / 2) : summit;
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new BedParser(rg.Columns);
var parsedPeak = parser.Parse(file.Path).Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.ToList()[0];
// Assert
Assert.True(parsedPeak.Summit == rg.Summit);
}
}
public void PValueConversion(double originalValue, double convertedValue, PValueFormats pvalueFormat)
{
// Arrange
var rg = new RegionGenerator {
Value = convertedValue
};
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new BedParser()
{
PValueFormat = pvalueFormat
};
var parsedData = parser.Parse(file.Path);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals[0].Value == originalValue);
}
}
public void PValueAssertion(double value, PValueFormats pvalueFormat, bool validate, bool expected)
{
// Arrange
var rg = new RegionGenerator {
Value = value
};
// Act
using (var file = new TempFileCreator(rg))
{
var parser = new BedParser()
{
PValueFormat = pvalueFormat,
ValidatePValue = validate
};
var parsedData = parser.Parse(file.Path);
// Assert
Assert.True(parsedData.Chromosomes.Any() == expected);
}
}
public void UseDefaultValueIfInvalidPValueColumn()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new BedParser(new BedColumns()
{
Value = 9
})
{
DropPeakIfInvalidValue = false
};
var parsedData = parser.Parse(file.Path);
// Assert
Assert.True(parsedData.Chromosomes.ContainsKey(rg.Chr));
}
}
public void TestExcessChrs(string chr)
{
// Arrange
var rg = new RegionGenerator {
Chr = chr
};
using (var file = new TempFileCreator(rg))
{
// Act
BedParser <Peak> parser = new BedParser()
{
Assembly = Assemblies.hg19,
ReadOnlyAssemblyChrs = false
};
parser.Parse(file.Path);
// Assert
Assert.True(parser.ExcessChrs.Count == 1);
}
}
public void TestMissingChrs()
{
// Arrange
var rg = new RegionGenerator {
Chr = "chr1"
};
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new BedParser()
{
Assembly = Assemblies.hg19,
ReadOnlyAssemblyChrs = false
};
parser.Parse(file.Path);
// Assert
Assert.True(parser.MissingChrs.Count == References.GetGenomeSizes(Assemblies.hg19).Count - 1);
}
}
public void DropLineIfInvalidChr(string chr)
{
// Arrange
var rg = new RegionGenerator {
Chr = chr
};
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new BedParser()
{
Assembly = Assemblies.hg19,
ReadOnlyAssemblyChrs = true
};
var parsedData = parser.Parse(file.Path);
// Assert
Assert.True(parsedData.Chromosomes.Count == 0);
}
}
public void ParseIntervalChrWhenChrPrefixIsMissing(string chr)
{
// Arrange
var rg = new RegionGenerator {
Chr = chr
};
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new BedParser()
{
Assembly = Assemblies.hg19,
ReadOnlyAssemblyChrs = true
};
var parsedData = parser.Parse(file.Path);
// Assert
Assert.True(parsedData.Chromosomes.ContainsKey("chr" + chr));
}
}
public void LogErrorIfFailedToReadALine()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new BedParser(new BedColumns()
{
Value = 9
})
{
DropPeakIfInvalidValue = true
};
var parsedData = parser.Parse(file.Path);
// Assert
Assert.True(parsedData.Messages.Count > 0);
}
}
public void InvalidNameColumn()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new BedParser(new BedColumns()
{
Name = 12
})
{
DropPeakIfInvalidValue = false
};
var parsedData = parser.Parse(file.Path);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals[0].Name == null);
}
}
public void TestDelimiter(char delimiter)
{
// Arrange
string chr = "chr1";
char strand = '*';
var rg = new RegionGenerator {
Chr = chr, Strand = strand
};
using (var file = new TempFileCreator(rg.GetSampleLine(delimiter)))
{
// Act
var parser = new BedParser()
{
Delimiter = delimiter
};
var parsedData = parser.Parse(file.Path);
// Assert
Assert.True(parsedData.Chromosomes[chr].Strands[strand].Intervals[0].CompareTo(rg.Peak) == 0);
}
}
public void ReadValueInvariantCulture(double value, string culture)
{
// Arrange
var rg = new RegionGenerator
{
Value = value,
Culture = culture
};
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new BedParser
{
Culture = culture
};
var parsedData = parser.Parse(file.Path);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.ToList()[0].Value == rg.Value);
}
}
public TempFileCreator(RegionGenerator columns, int headerLineCount = 0, int peaksCount = 1)
{
Path = System.IO.Path.GetTempPath() + Guid.NewGuid().ToString() + ".bed";
FileStream stream = File.Create(Path);
using (StreamWriter writer = new StreamWriter(stream))
{
while (headerLineCount-- > 0)
{
writer.WriteLine(columns.GetSampleHeader());
}
while (peaksCount-- > 0)
{
writer.WriteLine(columns.GetSampleLine());
if (peaksCount > 0)
{
columns.Left = columns.Right + 10;
columns.Right = columns.Right + 20;
}
}
}
}
public void ColumnsSetters()
{
// Arrange
var rg = new RegionGenerator
{
ChrColumn = 2,
LeftColumn = 2,
RightColumn = 9,
ValueColumn = 0,
SummitColumn = 2,
NameColumn = 2,
StrandColumn = 0,
};
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new BedParser(rg.Columns);
var parsedPeak = parser.Parse(file.Path).Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.ToList()[0];
// Assert
Assert.True(parsedPeak.CompareTo(rg.Peak) == 0);
}
}
