private void CreateShuffleRegions(string folderPath)
{
if (!Directory.Exists(folderPath + "sorted" + dirSep))
{
Directory.CreateDirectory(folderPath + "sorted" + dirSep);
}
using (FileStream fs =
new FileStream(folderPath + "sorted" + dirSep + "TESTONLY" + "." + filesExtension, FileMode.Append, FileAccess.Write))
using (StreamWriter sw = new StreamWriter(fs))
foreach (var coordinate in generatedCoordinatesFORTESTONLY)
{
sw.WriteLine(coordinate.Key.ToString() + "\t" + coordinate.Value.ToString());
}
Console.WriteLine("Writing shuffled files.");
string randomChr = null;
char randomStrand = 'V';
int randomRegion = 0;
Peak peak = null;
var dirInfo = new DirectoryInfo(folderPath + dirSep + "sorted");
FileInfo[] determinedFiles = dirInfo.GetFiles("*." + filesExtension);
foreach (FileInfo fileInfo in determinedFiles)
{
Console.WriteLine(string.Format("Now writing: {0}", Path.GetFileNameWithoutExtension(fileInfo.FullName)));
BEDParser <Peak, PeakData> bedParser = new BEDParser <Peak, PeakData>(fileInfo.FullName, Genomes.HomoSapiens, Assemblies.hg19, true);
var parsedSample = bedParser.Parse();
var intervals = parsedSample.intervals;
if (!Directory.Exists(folderPath + "shuffled" + dirSep))
{
Directory.CreateDirectory(folderPath + "shuffled" + dirSep);
}
using (FileStream fs =
new FileStream(folderPath + "shuffled" + dirSep + Path.GetFileNameWithoutExtension(fileInfo.FullName) + "." + filesExtension, FileMode.Append, FileAccess.Write))
using (StreamWriter sw = new StreamWriter(fs))
while (intervals.Count > 0)
{
randomChr = intervals.ElementAt(rnd.Next(0, intervals.Count)).Key;
randomStrand = intervals[randomChr].ElementAt(rnd.Next(0, intervals[randomChr].Count)).Key;
randomRegion = rnd.Next(0, intervals[randomChr][randomStrand].Count);
peak = intervals[randomChr][randomStrand][randomRegion];
sw.WriteLine(randomChr + "\t" + peak.ToString("\t") + "\t" + randomStrand);
intervals[randomChr][randomStrand].RemoveAt(randomRegion);
if (intervals[randomChr][randomStrand].Count == 0)
{
intervals[randomChr].Remove(randomStrand);
}
if (intervals[randomChr].Count == 0)
{
intervals.Remove(randomChr);
}
}
}
Console.WriteLine("Done");
}
