static void Main(string[] args)
{
try
{
Parser.Default.ParseArguments <Options>(args).WithParsed(options =>
{
if (options.Verbose)
{
SetVerboseLogging();
}
bool combine = options.Combine;
string dateTime = DateTime.Now.ToString("yyyy-MM-dd_hh-mm-ss");
List <string> inputFiles = new List <string>();
if (options.LoadFromDirectory != null && options.LoadFromDirectory == true)//multiple files
{
var directoryPath = Path.GetDirectoryName(options.InputFile);
DirectoryInfo di = new DirectoryInfo(directoryPath);
Logger.Info("Attempting to load files with the extension .mzml in the following directory: {0}", directoryPath);
foreach (var file in di.GetFiles("*.mzml", SearchOption.TopDirectoryOnly))
{
inputFiles.Add(file.FullName);
}
if (inputFiles.Count == 0)
{
Logger.Error("Unable to locate any MZML files in {0} directory", directoryPath);
throw new FileNotFoundException();
}
}
else //single file
{
inputFiles.Add(options.InputFile);
}
foreach (string inputFilePath in inputFiles)
{
bool lastFile = false;//saving whether its the last file or not, so if we need to combine all the files in the end, we know when the end is.
string fileSpecificDirectory = DirectoryCreator.CreateOutputDirectory(inputFilePath, dateTime);
if (inputFilePath == inputFiles.Last())
{
lastFile = true;
}
Logger.Info("Loading file: {0}", inputFilePath);
Stopwatch sw = new Stopwatch();
sw.Start();
int division;
if (options.Division < 100 && options.Division > 0)
{
division = options.Division;
}
else
{
Logger.Error("Number of divisions must be within the range 1 - 100. You have input: {0}", options.Division);
throw new ArgumentOutOfRangeException();
}
bool irt = !String.IsNullOrEmpty(options.IRTFile);
MzmlParser.MzmlReader mzmlParser = new MzmlParser.MzmlReader
{
ParseBinaryData = options.ParseBinaryData ?? true,
Threading = options.Threading ?? true,
MaxQueueSize = options.MaxQueueSize,
MaxThreads = options.MaxThreads
};
CheckFileIsReadableOrComplain(inputFilePath);
AnalysisSettings analysisSettings = new AnalysisSettings()
{
MassTolerance = options.MassTolerance,
RtTolerance = options.RtTolerance,
IrtMinIntensity = options.IrtMinIntensity,
IrtMinPeptides = options.IrtMinTransitions,
IrtMassTolerance = options.IrtMassTolerance,
CacheSpectraToDisk = options.Cache,
MinimumIntensity = options.MinimumIntensity,
RunEndTime = options.RunEndTime
};
if (!String.IsNullOrEmpty(options.IRTFile))
{
irt = true;
if (options.IRTFile.ToLower().EndsWith("traml", StringComparison.InvariantCultureIgnoreCase))
{
TraMLReader traMLReader = new TraMLReader();
analysisSettings.IrtLibrary = traMLReader.LoadLibrary(options.IRTFile);
}
else if (options.IRTFile.ToLower().EndsWith("tsv", StringComparison.InvariantCultureIgnoreCase) || options.IRTFile.ToLower().EndsWith("csv", StringComparison.InvariantCultureIgnoreCase))
{
SVReader svReader = new SVReader();
analysisSettings.IrtLibrary = svReader.LoadLibrary(options.IRTFile);
}
}
MzmlParser.Run run = mzmlParser.LoadMzml(inputFilePath, analysisSettings);
AnalysisSettingsFileWriter Aw = new AnalysisSettingsFileWriter();
if (inputFiles.Count() > 1 && lastFile)//multiple files and this is the last
{
Aw.WriteASFile(run, dateTime, inputFiles);
}
else //only one file
{
Aw.WriteASFile(run, dateTime, inputFilePath);
}
Logger.Info("Generating metrics...", Convert.ToInt32(sw.Elapsed.TotalSeconds));
var swameMetrics = new SwaMe.MetricGenerator().GenerateMetrics(run, division, inputFilePath, irt, combine, lastFile, dateTime);
var progMetrics = new Prognosticator.MetricGenerator().GenerateMetrics(run);
var metrics = swameMetrics.Union(progMetrics).ToDictionary(k => k.Key, v => v.Value);
string[] mzQCName = { dateTime, Path.GetFileNameWithoutExtension(inputFilePath), "mzQC.json" };
Directory.SetCurrentDirectory(fileSpecificDirectory);
new MzqcGenerator.MzqcWriter().BuildMzqcAndWrite(string.Join("_", mzQCName), run, metrics, inputFilePath);
Logger.Info("Generated metrics in {0} seconds", Convert.ToInt32(sw.Elapsed.TotalSeconds));
if (analysisSettings.CacheSpectraToDisk)
{
Logger.Info("Deleting temp files...");
mzmlParser.DeleteTempFiles(run);
}
Logger.Info("Done!");
}
});
}
catch (Exception ex)
{
Logger.Error("An unexpected error occured:");
Logger.Error(ex.Message);
Logger.Error(ex.StackTrace);
LogManager.Shutdown();
Environment.Exit(1);
}
LogManager.Shutdown();
Environment.Exit(0);
}
static void Main(string[] args)
{
try
{
Parser.Default.ParseArguments <Options>(args).WithParsed(options =>
{
// An inputfile of "-" on the command line denotes stdin, for which we use null internally.
if ("-".Equals(options.InputFile, StringComparison.Ordinal))
{
options.InputFile = null;
}
// An outputfile of "-" on the command line denotes stdout, for which we use null internally.
if ("-".Equals(options.OutputFile, StringComparison.Ordinal))
{
options.OutputFile = null;
}
if (options.Verbose)
{
SetVerboseLogging();
}
if (null == options.InputFile)
{
Logger.Info("Loading file: {0}", options.InputFile);
}
else
{
Logger.Info("Reading mzML from standard input");
}
Stopwatch sw = new Stopwatch();
sw.Start();
int division;
if (options.Division < 100 && options.Division > 0)
{
division = options.Division;
}
else
{
Logger.Error("Number of divisions must be within the range 1 - 100. You have input: {0}", options.Division);
throw new ArgumentOutOfRangeException();
}
bool irt = !string.IsNullOrEmpty(options.IRTFile);
// stdin (denoted by null) is always considered readable; anything else needs a check (#99)
if (null != options.InputFile)
{
CheckFileIsReadableOrComplain(options.InputFile);
}
AnalysisSettings analysisSettings = new AnalysisSettings()
{
MassTolerance = options.MassTolerance,
RtTolerance = options.RtTolerance,
IrtMinIntensity = options.IrtMinIntensity,
IrtMinPeptides = options.IrtMinTransitions,
IrtMassTolerance = options.IrtMassTolerance,
CacheSpectraToDisk = options.Cache,
MinimumIntensity = options.MinimumIntensity,
TempFolder = Path.Combine(options.TempFolder, Guid.NewGuid().ToString())
};
if (analysisSettings.CacheSpectraToDisk && !Directory.Exists(analysisSettings.TempFolder))
{
Directory.CreateDirectory(analysisSettings.TempFolder);
}
using Pipeliner pipeliner = new Pipeliner()
{
Threading = options.Threading ?? true,
MaxQueueSize = options.MaxQueueSize,
MaxThreads = options.MaxThreads
};
if (!string.IsNullOrEmpty(options.IRTFile))
{
irt = true;
if (options.IRTFile.ToLower().EndsWith("traml", StringComparison.InvariantCultureIgnoreCase))
{
TraMLReader traMLReader = new TraMLReader();
analysisSettings.IrtLibrary = traMLReader.LoadLibrary(options.IRTFile);
}
else if (options.IRTFile.ToLower().EndsWith("tsv", StringComparison.InvariantCultureIgnoreCase) || options.IRTFile.ToLower().EndsWith("csv", StringComparison.InvariantCultureIgnoreCase))
{
SVReader svReader = new SVReader();
analysisSettings.IrtLibrary = svReader.LoadLibrary(options.IRTFile);
}
}
using Run <Scan> run = pipeliner.LoadMzml(options.InputFile, analysisSettings);
Logger.Info("Generating metrics...", Convert.ToInt32(sw.Elapsed.TotalSeconds));
var swameMetrics = new SwaMe.MetricGenerator().GenerateMetrics(run, division, irt);
var progMetrics = new Prognosticator.MetricGenerator().GenerateMetrics(run);
var metrics = swameMetrics.Union(progMetrics).ToDictionary(k => k.Key, v => v.Value);
new MzqcGenerator.MzqcWriter().BuildMzqcAndWrite(options.OutputFile, run, metrics, options.InputFile, analysisSettings);
Logger.Info("Generated metrics in {0} seconds", Convert.ToInt32(sw.Elapsed.TotalSeconds));
if (analysisSettings.CacheSpectraToDisk)
{
Logger.Trace("Deleting temp files...");
Directory.Delete(analysisSettings.TempFolder);
}
Logger.Trace("Done!");
});
}
catch (Exception ex)
{
Logger.Fatal(ex, "An unexpected error occured");
Logger.Fatal(ex.Message);
Logger.Fatal(ex.StackTrace);
LogManager.Shutdown();
Environment.Exit(1);
}
LogManager.Shutdown();
Environment.Exit(0);
}
private void AnalyseSample()
{
string dateTime = DateTime.Now.ToString("yyyy-MM-dd_HH-mm-ss");
List <string> inputFiles = new List <string>();
Logger logger = LogManager.GetCurrentClassLogger();
bool lastFile = false;//saving whether its the last file or not, so if we need to combine all the files in the end, we know when the end is.
logger.Info("Loading file: {0}", inputFilePath);
Stopwatch sw = new Stopwatch();
sw.Start();
int division;
if (rtDivisionUpDown.Value < 100 && rtDivisionUpDown.Value > 0)
{
division = decimal.ToInt32(rtDivisionUpDown.Value);
}
else
{
logger.Error("Number of divisions must be within the range 1 - 100. You have input: {0}", rtDivisionUpDown.Value);
throw new ArgumentOutOfRangeException();
}
bool irt = !string.IsNullOrEmpty(irtFilePath);
Pipeliner pipeliner = new Pipeliner()
{
Threading = true,
MaxQueueSize = decimal.ToInt32(MaxQueueUpDown.Value),
MaxThreads = decimal.ToInt32(MaxThreadsUpDown.Value),
CancellationToken = _cts.Token
};
CheckFileIsReadableOrComplain(inputFilePath);
AnalysisSettings analysisSettings = new AnalysisSettings()
{
MassTolerance = decimal.ToDouble(BasePeakMassToleranceUpDown.Value),
RtTolerance = decimal.ToDouble(BasePeakRtToleranceUpDown.Value),
IrtMinIntensity = decimal.ToDouble(MinIrtIntensityUpDown.Value),
IrtMinPeptides = decimal.ToInt32(irtPeptidesUpDown.Value),
IrtMassTolerance = decimal.ToDouble(irtToleranceUpDown.Value),
CacheSpectraToDisk = CacheToDiskCheckBox.Checked,
MinimumIntensity = decimal.ToInt32(MinIrtIntensityUpDown.Value),
TempFolder = Path.Combine(Path.GetTempPath(), Guid.NewGuid().ToString())
};
if (analysisSettings.CacheSpectraToDisk && !Directory.Exists(analysisSettings.TempFolder))
{
Directory.CreateDirectory(analysisSettings.TempFolder);
}
if (!string.IsNullOrEmpty(irtFilePath))
{
irt = true;
if (irtFilePath.ToLower().EndsWith("traml", StringComparison.InvariantCultureIgnoreCase))
{
TraMLReader traMLReader = new TraMLReader();
analysisSettings.IrtLibrary = traMLReader.LoadLibrary(irtFilePath);
}
else if (irtFilePath.ToLower().EndsWith("tsv", StringComparison.InvariantCultureIgnoreCase) || irtFilePath.ToLower().EndsWith("csv", StringComparison.InvariantCultureIgnoreCase))
{
SVReader svReader = new SVReader();
analysisSettings.IrtLibrary = svReader.LoadLibrary(irtFilePath);
}
}
using (Run <Scan> run = pipeliner.LoadMzml(inputFilePath, analysisSettings))
{
AnalysisSettingsFileWriter Aw = new AnalysisSettingsFileWriter();
if (inputFiles.Count() > 1 && lastFile)//multiple files and this is the last
{
Aw.WriteASFile(run, dateTime, inputFiles);
}
else //only one file
{
Aw.WriteASFile(run, dateTime, inputFilePath);
}
logger.Info("Generating metrics...", Convert.ToInt32(sw.Elapsed.TotalSeconds));
var swameMetrics = new SwaMe.MetricGenerator().GenerateMetrics(run, division, irt);
var progMetrics = new Prognosticator.MetricGenerator().GenerateMetrics(run);
var metrics = swameMetrics.Union(progMetrics).ToDictionary(k => k.Key, v => v.Value);
new MzqcGenerator.MzqcWriter().BuildMzqcAndWrite("", run, metrics, inputFilePath, analysisSettings);
logger.Info("Generated metrics in {0} seconds", Convert.ToInt32(sw.Elapsed.TotalSeconds));
}
if (analysisSettings.CacheSpectraToDisk)
{
Directory.Delete(analysisSettings.TempFolder);
}
logger.Trace("Done!");
LogManager.Shutdown();
}