/// <summary>
/// Execute a local BLAST against a sequence database.
/// </summary>
/// <param name="db">Name of the BLAST database (use filename only).</param>
/// <param name="targetFasta">Filename of the input FASTA file.</param>
public void RunLocalBlast(string db, string targetFasta)
{
this.Blaster = new BlastLocalHandler();
#region BLAST parameters
IBlastParameters args;
if (db.Equals(Resource.UniVec) || db.Equals(Resource.UniVec_Core))
{
args = new UniVecParameters();
}
else
{
args = new BlastLocalParameters();
}
args.Database = db;
args.Threads = Environment.ProcessorCount;
string outputFilename = Path.ChangeExtension(targetFasta, Properties.Resource.BLAST_OUTPUT_SUFFIX_ASN);
#endregion
this.Blaster.ExecuteLocal(targetFasta, outputFilename, args);
// Convert to XML
string xmlFilename = Path.ChangeExtension(outputFilename, Resource.XmlExtension);
BlastTools.FormatASNTo("5", outputFilename, xmlFilename);
this.BlastHspCounter = BlastTools.ProcessBlastXml(xmlFilename);
// Convert to CSV
string csvFilename = Path.ChangeExtension(outputFilename, Resource.CsvExtension);
BlastTools.FormatASNTo("10", outputFilename, csvFilename);
}
/// <summary>
/// Constructor for OpenFileDialog
/// </summary>
/// <param name="fileTypes">List of valid file types</param>
public OpenFileDialog(List <string> fileTypes)
{
InitializeComponent();
this.btnBrowse.Focus();
#region Parser type combo box
// Populate the parser type combo box
ComboBoxItem defaultItem = new ComboBoxItem();
defaultItem.Content = Resource.MANUAL_CHOICE;
this.comboParserType.Items.Add(defaultItem);
Collection <string> validParsers = new Collection <string>();
validParsers.Add(SequenceParsers.FastQ.Name);
validParsers.Add(SequenceParsers.Fasta.Name);
foreach (var parserName in validParsers)
{
ComboBoxItem item = new ComboBoxItem();
item.Content = parserName;
item.Tag = parserName;
this.comboParserType.Items.Add(item);
}
this.comboParserType.SelectedIndex = 0;
this.fileTypes = fileTypes;
#endregion
#region FASTQ format combo box
defaultItem = new ComboBoxItem();
defaultItem.Content = Resource.MANUAL_CHOICE;
this.comboFastqType.Items.Add(defaultItem);
string[] validFormats = BioHelper.QueryValidFastqFormats();
foreach (var format in validFormats)
{
ComboBoxItem item = new ComboBoxItem();
item.Content = format;
item.Tag = format;
this.comboFastqType.Items.Add(item);
}
this.comboFastqType.SelectedIndex = 0;
#endregion
#region BLAST database combo box
this.availableBlastDatabases = new List <string> ();
// query for available BLAST databases
List <string> databases = BlastTools.QueryAvailableBlastDatabases();
foreach (var db in databases)
{
ComboBoxItem item = new ComboBoxItem();
item.Content = db;
item.Tag = db;
this.comboBlastDb.Items.Add(item);
}
this.comboBlastDb.SelectedIndex = 0;
#endregion
}
