public RegionGenerator()
{
// NOTE
// The following default column indexes must match the
// BED file type specifications. These specifications can
// be obtained from various resources such as Ensemble:
// https://uswest.ensembl.org/info/website/upload/bed.html
Columns = new BedColumns()
{
Chr = 0,
Left = 1,
Right = 2,
Name = 3,
Value = 4,
Strand = -1,
Summit = -1
};
Chr = "chr1";
Left = 10;
Right = 20;
Summit = 15;
Name = "GeUtilities_01";
Value = 0.12345;
Strand = '.';
Culture = CultureInfo.CurrentCulture.Name;
}
/// <summary>
/// Parse standard Browser Extensible Data (BED) format.
/// </summary>
/// <param name="sourceFilePath">Full path of source file name.</param>
public BedParser(BedColumns columns, IPeakConstructor <I> constructor) : base(columns)
{
_constructor = constructor;
_nameColumn = columns.Name;
_valueColumn = columns.Value;
_summitColumn = columns.Summit;
_mostStringentPeak = _constructor.Construct(0, 2, 1);
_mostPermissivePeak = _constructor.Construct(0, 2, 0);
DefaultValue = 1E-8;
DropPeakIfInvalidValue = true;
ValidatePValue = true;
PValueFormat = PValueFormats.SameAsInput;
}
public BedParser(BedColumns columns) : base(columns, new PeakConstructor())
{
}
public void ParseBasedOnGivenParserConfig()
{
// Arrange
string rep1Path = Path.GetTempPath() + Guid.NewGuid().ToString() + ".bed";
string rep2Path = Path.GetTempPath() + Guid.NewGuid().ToString() + ".bed";
FileStream stream = File.Create(rep1Path);
using (StreamWriter writter = new StreamWriter(stream))
{
writter.WriteLine("ABC\t____\t10\t+++++\t100.0\tchr1\t___====____\tmspc_peak_1\t20");
writter.WriteLine("ABC\t____\t25\t+++++\t123.4\tchr1\t___====____\tmspc_peak_2\t35");
}
stream = File.Create(rep2Path);
using (StreamWriter writter = new StreamWriter(stream))
{
writter.WriteLine("ABC\t____\t11\t+++++\t31.4\tchr1\t___====____\tmspc_peak_3\t18");
writter.WriteLine("ABC\t____\t22\t+++++\t21.4\tchr1\t___====____\tmspc_peak_4\t28");
writter.WriteLine("ABC\t____\t30\t+++++\t99.9\tchr1\t___====____\tmspc_peak_5\t40");
}
var cols = new BedColumns()
{
Chr = 5,
Left = 2,
Right = 8,
Name = 7,
Strand = -1,
Summit = -1
};
var path = Environment.CurrentDirectory + Path.DirectorySeparatorChar + "MSPCTests_" + new Random().NextDouble().ToString();
using (StreamWriter w = new StreamWriter(path))
w.WriteLine(JsonConvert.SerializeObject(cols));
// Act
string console = null;
using (StringWriter sw = new StringWriter())
{
Console.SetOut(sw);
Program.Main(string.Format("-i {0} -i {1} -r bio -w 1E-1 -s 1E-4 -c 1 -p {2}", rep1Path, rep2Path, path).Split(' '));
File.Delete(rep1Path);
File.Delete(rep2Path);
console = sw.ToString();
}
// Assert
Assert.Contains("Read peaks#:\t2", console);
Assert.Contains("Read peaks#:\t3", console);
Assert.Contains("Max p-value:\t1.000E-100", console);
Assert.Contains("Min p-value:\t3.981E-124", console);
Assert.Contains("Min p-value:\t1.259E-100", console);
Assert.Contains("Max p-value:\t3.981E-022", console);
// Clean up
File.Delete(rep1Path);
File.Delete(rep2Path);
foreach (var p in Directory.GetDirectories(Environment.CurrentDirectory, "session_*"))
{
Directory.Delete(p, true);
}
}
