public void TestColumnsShuffle(
byte chrColumn,
byte leftColumn,
sbyte rightColumn,
byte refSeqIDColumn,
byte geneSymbolColumn,
sbyte strandColumn)
{
// Arrange
var rg = new RegionGenerator()
{
ChrColumn = chrColumn,
LeftColumn = leftColumn,
RightColumn = rightColumn,
RefSeqIDColumn = refSeqIDColumn,
GeneSymbolColumn = geneSymbolColumn,
StrandColumn = strandColumn
};
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new RefSeqParser(rg.Columns);
var parsedGene = parser.Parse(file.TempFilePath).Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.ToList()[0];
// Assert
Assert.True(parsedGene.CompareTo(rg.Gene) == 0);
}
}
public void AssignHashKey()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new RefSeqParser();
var parsedData = parser.Parse(file.TempFilePath);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals[0].GetHashCode() != 0);
}
}
public void TestDefaultRefSeqGenesColumnOrder()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new RefSeqParser();
var parsedGene = parser.Parse(file.TempFilePath).Chromosomes[rg.Chr].Strands[rg.Strand].Intervals[0];
// Assert
Assert.True(parsedGene.CompareTo(rg.Gene) == 0);
}
}
public void FullySetArguments()
{
// Arrange
var rg = new RegionGenerator();
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new RefSeqParser(rg.Columns);
var parsedGene = parser.Parse(file.TempFilePath).Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.ToList()[0];
// Assert
Assert.True(parsedGene.CompareTo(rg.Gene) == 0);
}
}
public void ReadRefSeqID()
{
// Arrange
var rg = new RegionGenerator {
RefSeqID = "RefSeqID_001"
};
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new RefSeqParser();
var parsedData = parser.Parse(file.TempFilePath);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals[0].RefSeqID == rg.RefSeqID);
}
}
public void FailReadChr(string chr)
{
// Arrange
var rg = new RegionGenerator {
Chr = "chr1"
};
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new RefSeqParser();
var parsedData = parser.Parse(file.TempFilePath);
// Assert
Assert.False(parsedData.Chromosomes.ContainsKey(chr));
}
}
public void ReadGeneSymbol()
{
// Arrange
var rg = new RegionGenerator {
GeneSymbol = "Symbol_001"
};
using (var file = new TempFileCreator(rg))
{
// Act
var parser = new RefSeqParser();
var parsedData = parser.Parse(file.TempFilePath);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.ToList()[0].GeneSymbol == rg.GeneSymbol);
}
}
public void MultiFeatureFile()
{
// Arrange
var rg = new RegionGenerator {
StrandColumn = 12
};
using (var file = new TempFileCreator(rg, genesCount: 10, headerLineCount: 2))
{
// Act
var parser = new RefSeqParser();
var parsedData = parser.Parse(file.TempFilePath);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands[rg.Strand].Intervals.Count == 10);
}
}
public TempFileCreator(RegionGenerator columns, int headerLineCount = 0, int genesCount = 1)
{
TempFilePath = Path.GetTempPath() + Guid.NewGuid().ToString() + ".refSeq";
FileStream stream = File.Create(TempFilePath);
using (StreamWriter writer = new StreamWriter(stream))
{
while (headerLineCount-- > 0)
{
writer.WriteLine(columns.GetSampleHeader());
}
while (genesCount-- > 0)
{
writer.WriteLine(columns.GetSampleLine());
}
}
}
public void ReadStrand(char strand)
{
// Arrange
var rg = new RegionGenerator
{
Strand = strand,
StrandColumn = 5
};
using (var file = new TempFileCreator(rg))
{
// Act
var genesParser = new RefSeqParser(rg.Columns);
var parsedData = genesParser.Parse(file.TempFilePath);
// Assert
Assert.True(parsedData.Chromosomes[rg.Chr].Strands.ContainsKey(strand));
}
}
