private bool LoadParserConfig(CommandLineOptions options, out ParserConfig config)
{
config = new ParserConfig();
if (options.ParserConfig != null)
{
try
{
config = ParserConfig.LoadFromJSON(options.ParserConfig);
if (config == null)
{
_logger.LogException(string.Format(
"error reading parser configuration JSON object, " +
"check if the given file '{0}' exists and is accessible.",
options.ParserConfig));
return(false);
}
}
catch (Exception e)
{
_logger.LogException("error reading parser configuration JSON object: " + e.Message);
Environment.ExitCode = 1;
return(false);
}
}
return(true);
}
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);
}
private bool ParseFiles(IReadOnlyList <string> files, ParserConfig parserConfig, out List <Bed <Peak> > samples)
{
try
{
samples = new List <Bed <Peak> >();
_logger.LogStartOfASection("Parsing Samples");
_logger.InitializeLoggingParser(files.Count);
int counter = 0;
foreach (var file in files)
{
var bedParser = new BedParser(parserConfig)
{
PValueFormat = parserConfig.PValueFormat,
DefaultValue = parserConfig.DefaultValue,
DropPeakIfInvalidValue = parserConfig.DropPeakIfInvalidValue,
Culture = parserConfig.Culture
};
var parsedData = bedParser.Parse(file);
samples.Add(parsedData);
counter++;
_logger.LogParser(
counter,
files.Count,
file,
parsedData.IntervalsCount,
parsedData.PValueMin.Value,
parsedData.PValueMean,
parsedData.PValueMax.Value);
}
return(true);
}
catch (Exception e)
{
samples = null;
_logger.LogException("error parsing data: " + e.Message);
Environment.ExitCode = 1;
return(false);
}
}
public static void Main(string[] args)
{
string mspcCannotContinue = "\r\nMSPC cannot continue.";
var cliOptions = new CommandLineOptions();
try
{
cliOptions.Parse(args, out bool helpIsDisplayed);
if (helpIsDisplayed)
{
return;
}
}
catch (Exception e)
{
Console.WriteLine(e.Message + mspcCannotContinue);
return;
}
if (cliOptions.Input.Count < 2)
{
Console.WriteLine(string.Format(
"At least two samples are required; {0} is given.{1}",
cliOptions.Input.Count, mspcCannotContinue));
return;
}
foreach (var file in cliOptions.Input)
{
if (!File.Exists(file))
{
Console.WriteLine(string.Format("Missing file: {0}{1}", file, mspcCannotContinue));
return;
}
}
var orchestrator = new Orchestrator(cliOptions.Options);
var parserConfig = new ParserConfig();
if (cliOptions.ParserConfig != null)
{
parserConfig = ParserConfig.LoadFromJSON(cliOptions.ParserConfig);
}
var et = new Stopwatch();
foreach (var file in cliOptions.Input)
{
Console.WriteLine(string.Format("Parsing sample: {0}", file));
et.Restart();
var parsedSample = orchestrator.LoadSample(file, parserConfig);
et.Stop();
Console.WriteLine("Done... ET:\t{0}", et.Elapsed.ToString());
Console.WriteLine("Read peaks#:\t{0}", parsedSample.IntervalsCount.ToString("N0", CultureInfo.InvariantCulture));
Console.WriteLine("Min p-value:\t{0}", string.Format("{0:E3}", parsedSample.PValueMin.Value));
Console.WriteLine("Max p-value:\t{0}", string.Format("{0:E3}", parsedSample.PValueMax.Value));
Console.WriteLine("");
}
Console.WriteLine("Analysis started ...");
et.Restart();
orchestrator.Run();
Console.WriteLine("\n\rSaving results ...");
orchestrator.Export();
et.Stop();
Console.WriteLine(" ");
Console.WriteLine(string.Format("All processes successfully finished [Analysis ET: {0}]", et.Elapsed.ToString()));
Console.WriteLine(" ");
orchestrator.WriteSummaryStats();
}