/// <summary>
/// Run the QC application module
/// </summary>
/// <param name="file"></param>
private void Run(CommandLineOptions myArgs)
{
#region Determine parser
// Determine parser type
InputSubmission input = new InputSubmission(myArgs.InputFile);
input.DetermineParserUtil();
if (input.Parser is Bio.IO.FastQ.FastQParser &&
myArgs.FastqFormat == null)
{
myArgs.ErrorWriteLine("For FASTQ input, please provide a valid FASTQ format: [Sanger, Solexa, Illumina]");
}
#endregion
myArgs.WriteLine("Processing the file " + myArgs.InputFile +
"...this may take a while depending on the input size. Please be patient!");
Stopwatch sw = new Stopwatch();
sw.Start();
#region Run QC analysis
// Run QC analysis
try
{
qcm = new Seqcos(input.Parser, myArgs.InputFile, myArgs.ExecuteSequenceQc, myArgs.ExecuteQualityScoreQc, myArgs.ExecuteBlast, myArgs.FastqFormat, dir: myArgs.OutputDirectory);
}
catch (ArgumentNullException e)
{
myArgs.ErrorWriteLine(e.Message);
}
myArgs.WriteLine("Performing sequence-level QC...");
qcm.SequenceQc.Process();
var time = ElapsedSeconds(sw);
Console.WriteLine(time.ToString() + " s");
if (!(input.Parser is FastAParser))
{
myArgs.WriteLine("Performing quality score-level QC...");
qcm.QualityScoreQc.Process();
time = ElapsedSeconds(sw, (long)time);
Console.WriteLine(time.ToString() + " s");
}
#endregion
#region Display statistics to console
if (!myArgs.silent)
{
qcm.WriteInputStatistics(myArgs.UseExcelHyperlinks);
DisplayInputStatistics();
}
#endregion
#region Generate plots
myArgs.WriteLine("Generating plots and saving them to: " + qcm.OutputDirectory);
// Do these last, so that after plotting each section you can't free up memory
qcm.PlotSequenceLevelStats();
qcm.FinishSequenceQc(); // free up some memory, since we won't be using this anymore
if (!(input.Parser is FastAParser))
{
qcm.PlotQualityScoreLevelStats();
qcm.FinishQualityScoreQC();
}
#endregion
#region Carry out BLAST analysis
if (myArgs.ExecuteBlast)
{
myArgs.WriteLine("Searching for contaminants...");
// Convert FASTQ to FASTA
string targetFasta = qcm.OutputDirectory + "/" + qcm.GetPrefix() + ".fa";
BioHelper.ConvertToFASTA(qcm.ContaminationFinder.TargetSequences, targetFasta, myArgs.BlastSize, overwrite: true);
// Run local NCBI BLAST
qcm.ContaminationFinder.RunLocalBlast(myArgs.BlastDbPrefix, targetFasta);
time = ElapsedSeconds(sw, (long)time);
Console.WriteLine(time.ToString() + " s");
File.Delete(targetFasta);
if (!myArgs.silent)
{
HighlightText("NCBI BLAST results from searching against " + myArgs.BlastDbPrefix + " database:\n");
DisplayBlastResults();
}
}
#endregion
input.Parser.Close();
sw.Stop();
myArgs.WriteLine("\nTotal time: " + ToSeconds(sw.ElapsedMilliseconds) + " s");
}
/// <summary>
/// This event is fired by analysisThread when the thread is invoked.
/// This event calls the main Qc application framework and executes the analysis.
/// </summary>
/// <param name="sender">BackgroundWorker instance</param>
/// <param name="e">Event parameters</param>
private void DoQcAnalysis(object sender, DoWorkEventArgs e)
{
BackgroundWorker worker = sender as BackgroundWorker;
if (worker != null)
{
try
{
OpenFileArgs args = e.Argument as OpenFileArgs;
System.Windows.Threading.Dispatcher dispatcher = run.Dispatcher;
UpdateProgressDelegate update = new UpdateProgressDelegate(UpdateProgressText);
if (args != null)
{
dispatcher.BeginInvoke(update, 0, "Starting analysis...please be patient!");
application = new Seqcos(args.InputInfo.Parser, args.InputInfo.Filename, args.CanRunSequenceQc, args.CanRunQualityScoreQc, args.CanRunBlast, args.FastqFormat);
#region Sequence-level QC
/// Run sequence level QC
if (args.CanRunSequenceQc)
{
// Content by position
dispatcher.BeginInvoke(update, 25, "Performing sequence-level QC...analyzing base positions");
application.SequenceQc.ContentByPosition();
dispatcher.BeginInvoke(update, 45, "Performing sequence-level QC...analyzing base positions");
application.SequenceQc.GCContentByPosition();
System.Threading.Thread.Sleep(100);
if (worker.CancellationPending)
{
e.Cancel = true;
return;
}
// Content by sequence
dispatcher.BeginInvoke(update, 65, "Performing sequence-level QC...analyzing sequences");
application.SequenceQc.ContentBySequence();
dispatcher.BeginInvoke(update, 85, "Performing sequence-level QC...analyzing sequences");
System.Threading.Thread.Sleep(100);
if (worker.CancellationPending)
{
e.Cancel = true;
return;
}
// Plot results
dispatcher.BeginInvoke(update, 80, "Generating plots...");
application.PlotSequenceLevelStats();
System.Threading.Thread.Sleep(100);
if (worker.CancellationPending)
{
e.Cancel = true;
return;
}
dispatcher.Invoke(System.Windows.Threading.DispatcherPriority.Send, update, 100, "Done sequence-level QC!");
}
#endregion
#region Quality score-level QC
/// Run quality score level QC
if (args.CanRunQualityScoreQc)
{
dispatcher.BeginInvoke(update, 5, "Performing quality score-level QC...analyzing base positions");
application.QualityScoreQc.ContentByPosition();
System.Threading.Thread.Sleep(100);
if (worker.CancellationPending)
{
e.Cancel = true;
return;
}
dispatcher.BeginInvoke(update, 25, "Performing quality score-level QC...analyzing sequences");
application.QualityScoreQc.ContentBySequence();
System.Threading.Thread.Sleep(100);
if (worker.CancellationPending)
{
e.Cancel = true;
return;
}
dispatcher.BeginInvoke(update, 55, "Generating plots (the boxplot will take a while...please be patient!)");
application.PlotQualityScoreLevelStats();
System.Threading.Thread.Sleep(100);
if (worker.CancellationPending)
{
e.Cancel = true;
return;
}
dispatcher.Invoke(System.Windows.Threading.DispatcherPriority.Send, update, 100, "Done quality score-level QC!");
}
application.WriteInputStatistics(excelFormat: false);
application.FinishQualityScoreQC();
#endregion
#region BLAST
/// Run BLAST
if (args.CanRunBlast)
{
dispatcher.BeginInvoke(update, 10, "Generating temporary FASTA file for BLAST...");
// execute BLAST here..
string targetFasta = application.OutputDirectory + "/" + application.GetPrefix() + ".fa";
BioHelper.ConvertToFASTA(application.ContaminationFinder.TargetSequences, targetFasta, args.BlastArgs.NumInputSequences, false);
dispatcher.BeginInvoke(update, 70, "Running BLAST...");
application.ContaminationFinder.RunLocalBlast(args.BlastArgs.Database, targetFasta);
dispatcher.BeginInvoke(update, 100, "Finished! Deleting FASTA file...");
File.Delete(targetFasta);
}
#endregion
}
}
catch (ArgumentNullException ex)
{
e.Cancel = true;
if (worker.CancellationPending)
{
return;
}
MessageBox.Show(ex.TargetSite + ": " + ex.Message);
}
catch (Exception ex)
{
e.Cancel = true;
if (worker.CancellationPending)
{
return;
}
MessageBox.Show(ex.TargetSite + ": " + ex.Message);
}
}
}