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");
}
private bool Load(string fileName)
{
if (!ValidateFileName(fileName, out fileName))
{
return(false);
}
_parserSTW.Restart();
BEDParser <Peak, PeakData> bedParser = new BEDParser <Peak, PeakData>(
source: fileName,
species: Genomes.HomoSapiens,
assembly: Assemblies.hg19,
readOnlyValidChrs: true,
startOffset: 0,
chrColumn: UserConfig.ParserParameters.chrColumn,
leftEndColumn: UserConfig.ParserParameters.leftEndColumn,
rightEndColumn: UserConfig.ParserParameters.rightEndColumn,
summitColumn: -1,
nameColumn: UserConfig.ParserParameters.nameColumn,
valueColumn: UserConfig.ParserParameters.valueColumn,
strandColumn: -1,
defaultValue: 0.01,
pValueFormat: pValueFormat.minus10_Log10_pValue,
dropPeakIfInvalidValue: false,
hashFunction: HashFunction.FNV);
try { Repository.parsedSample = bedParser.Parse(); }
catch (Exception e)
{
if (Path.GetDirectoryName(fileName) + Path.DirectorySeparatorChar == _workingDirectory &&
Path.GetExtension(fileName) == _logFile)
{
Herald.Announce(Herald.MessageType.Error, string.Format("The requested extension should not have same extension as the log file."));
}
else
{
Herald.Announce(Herald.MessageType.Error, string.Format("{0}", e.Message));
}
return(false);
}
_parserSTW.Stop();
_accumulatedLoadET += _parserSTW.Elapsed.TotalSeconds;
Herald.AnnounceExeReport("Loaded", new ExecutionReport(Repository.parsedSample.intervalsCount, _parserSTW.Elapsed));
return(true);
}
internal static ParsedChIPseqPeaks <int, Peak, Metadata> LoadSample(string arg)
{
BEDParser <Peak, Metadata> bedParser =
new BEDParser <Peak, Metadata>(
source: arg,
species: Genomes.HomoSapiens,
assembly: Assemblies.hg19,
readOnlyValidChrs: false,
startOffset: 0,
chrColumn: 0,
leftEndColumn: 1,
rightEndColumn: 2,
nameColumn: 3,
summitColumn: -1,
valueColumn: 4,
strandColumn: -1,
defaultValue: 0.1,
pValueFormat: pValueFormat.minus1_Log10_pValue,
dropPeakIfInvalidValue: true);
return(bedParser.Parse());
}
