public void TestMultiStrand()
{
// Arrange
string[] peaks = new string[]
{
"chr1\t10\t20\t*\tGeUtilities_00\t0.1",
"chr1\t30\t40\t+\tGeUtilities_01\t0.11",
"chr1\t50\t60\t-\tGeUtilities_02\t0.111",
"chr1\t50\t60\t#\tGeUtilities_02\t0.111", // Any strand name other than '+', '-', and '*' will be parsed as '*'.
};
using (var file = new TempFileCreator(peaks))
{
// Act
var parser = new BedParser(
new BedColumns
{
Chr = 0,
Left = 1,
Right = 2,
Strand = 3,
Name = 4,
Value = 5
});
var parsedData = parser.Parse(file.Path);
// Assert
Assert.True(parsedData.Chromosomes["chr1"].Strands.ContainsKey('*'));
Assert.True(parsedData.Chromosomes["chr1"].Strands.ContainsKey('+'));
Assert.True(parsedData.Chromosomes["chr1"].Strands.ContainsKey('-'));
Assert.False(parsedData.Chromosomes["chr1"].Strands.ContainsKey('#'));
}
}
public void CountNumberOfExportedPeaksInEachSet(uint sampleID, Attributes attribute, int count)
{
// Arrange & Act
string path = RunMSPCAndExportResults();
var sampleFolder = Array.Find(Directory.GetDirectories(path), (string f) => { return(f.Contains(_sidfm[sampleID])); });
var file = Array.Find(Directory.GetFiles(sampleFolder), (string f) => { return(Path.GetFileNameWithoutExtension(f).Equals(attribute.ToString())); });
var bedParser = new BedParser
{
PValueFormat = PValueFormats.minus1_Log10_pValue
};
var parsedSample = bedParser.Parse(file);
// Assert
if (count == 0)
{
Assert.False(parsedSample.Chromosomes.ContainsKey(_chr));
}
else
{
Assert.True(parsedSample.Chromosomes[_chr].Strands[_strand].Intervals.Count == count);
}
// Clean up
Directory.Delete(path, true);
}
public void TestMinMaxValueWhenDefaultValueIsUsed()
{
// Arrange
double defaultValue = 1e-8;
string[] peaks = new string[]
{
"chr1\t10\t20",
"chr1\t30\t40",
"chr1\t50\t60",
"chr1\t70\t80",
};
using (var file = new TempFileCreator(peaks))
{
// Act
var parser = new BedParser()
{
DropPeakIfInvalidValue = false,
DefaultValue = defaultValue
};
var parsedData = parser.Parse(file.Path);
// Assert
Assert.True(parsedData.PValueMax.Value == defaultValue);
Assert.True(parsedData.PValueMin.Value == defaultValue);
}
}
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 TestNullFilePath()
{
// Arrange
var parser = new BedParser();
// Act & Assert
Assert.Throws <ArgumentNullException>(() => parser.Parse(null));
}
public void FailReadValue()
{
// Arrange
using (var file = new TempFileCreator("chr1\t10\t20\tGeUtilities_01\t123..45"))
{
// Act
var parser = new BedParser();
var parsedData = parser.Parse(file.Path);
// Assert
Assert.False(parsedData.Chromosomes.ContainsKey("chr1"));
}
}
public void CompletedVCF()
{
// Arrange
using (var file = new Vcf.TempFileCreator(new Vcf.RegionGenerator()))
{
// Act
var parser = new BedParser();
parser.Parse(file.TempFilePath);
// Assert
Assert.True(parser.Status == "100");
}
}
public void InvalidFile()
{
// Arrange
string fileName = "a_file_name_which_does_not_exist_1234567890";
var parser = new BedParser();
// Act
Exception exception = Assert.Throws <FileNotFoundException>(() => parser.Parse(fileName));
// Assert
Assert.False(string.IsNullOrEmpty(exception.Message));
Assert.Equal(string.Format("The file `{0}` does not exist or is inaccessible.", fileName), exception.Message);
}
public void AvoidEmptyLines()
{
// Arrange
using (var file = new TempFileCreator(" "))
{
// Act
var parser = new BedParser();
var parsedData = parser.Parse(file.Path);
// Assert
Assert.True(parsedData.Chromosomes.Count == 0);
}
}
public Bed <Peak> LoadSample(string fileName, ParserConfig parserConfig)
{
var bedParser = new BedParser(parserConfig)
{
PValueFormat = parserConfig.PValueFormat,
DefaultValue = parserConfig.DefaultValue,
DropPeakIfInvalidValue = parserConfig.DropPeakIfInvalidValue
};
var parsedSample = bedParser.Parse(fileName);
_samples.Add(parsedSample);
return(parsedSample);
}
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));
}
}
public void Progress()
{
// Arrange
_previousStatus = -1;
using (var file = new Bed.TempFileCreator(new Bed.RegionGenerator(), peaksCount: 50))
{
// Act
var bedParser = new BedParser();
bedParser.StatusChanged += ParserStatusChanged;
bedParser.Parse(file.Path);
// Asserted in 'ParserStatusChanged'
}
}
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 FailReadChr(string chr)
{
// Arrange
using (var file = new TempFileCreator(new RegionGenerator {
Chr = "chr1"
}))
{
// Act
var parser = new BedParser();
var parsedData = parser.Parse(file.Path);
// Assert
Assert.False(parsedData.Chromosomes.ContainsKey(chr));
}
}
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 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 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 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 DropPeaksHavingInvalidPValue()
{
// Arrange
using (var file = new TempFileCreator("chr1\t10\t20\tGeUtilities_01\t123..45"))
{
// Act
var parser = new BedParser()
{
DropPeakIfInvalidValue = true
};
var parsedData = parser.Parse(file.Path);
// Assert
Assert.False(parsedData.Chromosomes.ContainsKey("chr1"));
}
}
public void FailReadRightColumnIndexOutOfRange()
{
// Arrange
using (var file = new TempFileCreator("chr1\t10\t20\tGeUtilities_01\t123.4"))
{
// Act
var parser = new BedParser(new BedColumns()
{
Right = 10
});
var parsedData = parser.Parse(file.Path);
// Assert
Assert.False(parsedData.Chromosomes.ContainsKey("chr1"));
}
}
public void AvoidHeader(int headerCount, byte readOffset)
{
// Arrange
using (var file = new TempFileCreator(new RegionGenerator(), headerLineCount: headerCount))
{
// Act
var parser = new BedParser()
{
ReadOffset = readOffset
};
var parsedData = parser.Parse(file.Path);
// Assert
Assert.True(parsedData.Chromosomes.Count == 1);
}
}
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 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 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 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 UseDefaultPValueForPeaksWithInvalidPValue()
{
// Arrange
double defaultValue = 0.112233;
using (var file = new TempFileCreator("chr1\t10\t20\tGeUtilities_01\t123..45"))
{
// Act
var parser = new BedParser()
{
DropPeakIfInvalidValue = false,
DefaultValue = defaultValue
};
var parsedData = parser.Parse(file.Path);
// Assert
Assert.True(parsedData.Chromosomes["chr1"].Strands['*'].Intervals[0].Value == defaultValue);
}
}