/// <summary>
/// Execute a local BLAST
/// </summary>
/// <param name="query">The query file in FASTA format</param>
/// <param name="output">The name of the BLAST output file</param>
public void ExecuteLocal(string query, string output, IBlastParameters args)
{
// Validate parameters
string commandArguments = BlastTools.FormatBlastArguments(query, output, args);
// Start the process
ProcessStartInfo psi = new ProcessStartInfo
{
FileName = this.BlastExe,
Arguments = commandArguments,
UseShellExecute = false,
RedirectStandardOutput = true,
RedirectStandardError = true
};
using (Process p = Process.Start(psi))
{
using (StreamReader reader = p.StandardOutput)
{
string resultStdOut = reader.ReadToEnd();
Console.Write(resultStdOut);
}
using (StreamReader error = p.StandardError)
{
string resultStdErr = error.ReadToEnd();
Console.Error.Write(resultStdErr);
}
}
this.QueryFilename = query;
this.DbFilename = args.Database;
this.OutputFilename = output;
}
/// <summary>
/// Format BLAST arguments to string
/// </summary>
/// <returns>Arguments formatted for command-line execution</returns>
public static string FormatBlastArguments(string query, string output, IBlastParameters args)
{
// Check if query file exists
if (!File.Exists(query))
{
throw new FileNotFoundException(Properties.Resource.FileNotFound, query);
}
StringBuilder str = new StringBuilder();
str.Append(FormatArgument("-db", InDoubleQuotes(args.Database)));
str.Append(FormatArgument("-query", InDoubleQuotes(query), true));
str.Append(FormatArgument("-out", InDoubleQuotes(output), true));
if (args.GapOpen != int.MaxValue)
{
str.Append(FormatArgument("-gapopen", args.GapOpen.ToString(), true));
}
if (args.GapExtend != int.MaxValue)
{
str.Append(FormatArgument("-gapextend", args.GapExtend.ToString(), true));
}
if (args.Mismatch <= 0)
{
str.Append(FormatArgument("-penalty", args.Mismatch.ToString(), true));
}
if (args.EValue != int.MaxValue)
{
str.Append(FormatArgument("-evalue", args.EValue.ToString(), true));
}
str.Append(FormatArgument("-outfmt", args.OutputFormat.ToString(), true));
str.Append(FormatArgument("-num_threads", args.Threads.ToString(), true));
return(str.ToString());
}
/// <summary>
/// When clicked, proceed to the analysis step.
/// </summary>
/// <param name="sender">Framework element.</param>
/// <param name="e">Routed event args</param>
private void OnRunClicked(object sender, RoutedEventArgs e)
{
// Store BLAST parameters
this.blastArgs = null;
if (this.blastEnabledCheckBox.IsChecked.Value)
{
this.blastArgs = new UniVecParameters();
this.blastArgs.Database = ((ComboBoxItem)this.comboBlastDb.SelectedItem).Content as string;
this.blastArgs.NumInputSequences = Convert.ToInt32(this.textBlastMaxSequences.Text);
}
OpenFileArgs runArgs = new OpenFileArgs(this.input, this.sequenceCheckBox.IsChecked.Value, this.qualityScoreCheckBox.IsChecked.Value, blastArgs, ((ComboBoxItem)this.comboFastqType.SelectedItem).Content.ToString());
// Hide this wondow
this.Visibility = System.Windows.Visibility.Hidden;
if (this.PrepareRun != null)
{
this.PrepareRun(sender, runArgs);
}
}
public OpenFileArgs(InputSubmission input, bool runSequenceQc, bool runQualityScoreQc, IBlastParameters blast, string format)
{
this.InputInfo = input;
this.CanRunSequenceQc = runSequenceQc;
this.CanRunQualityScoreQc = runQualityScoreQc;
this.BlastArgs = blast;
this.FastqFormat = format;
}
