public void QueryValidFastqFormatsTest()
{
string[] expected = new string[] { "Illumina", "Solexa", "Sanger" };
string[] actual;
actual = BioHelper.QueryValidFastqFormats();
Assert.AreEqual(expected.Length, actual.Length);
foreach (string format in actual)
{
Assert.IsTrue(expected.Any(s => s.Equals(format)));
}
}
/// <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
}
/// <summary>
/// Parse command line arguments
/// </summary>
/// <param name="args"></param>
/// <returns></returns>
static CommandLineOptions ProcessCommandLine(string[] args)
{
CommandLineOptions myArgs = new CommandLineOptions();
CommandLineArguments parser = new CommandLineArguments();
AddParameters(parser);
try
{
parser.Parse(args, myArgs);
}
catch (Exception e)
{
Console.Error.WriteLine("\nException while processing command line arguments [{0}]", e.Message);
Environment.Exit(-1);
}
if (myArgs.help)
{
string[] validFastqFormats = BioHelper.QueryValidFastqFormats();
string helpString = "Usage: SeqcosUtil.exe [options] <input file>\n"
+ "\nDescription: Evaluates the quality of sequencing reads and summarizes\n"
+ " the results in the form of text and plots. BLAST may be optionally performed\n"
+ " against a custom database (i.e. when looking for sequence contamination)."
+ "\n\n/help (/h)\n Show this help information"
+ "\n\n/silent (/s)\n Show less details displayed in the console"
+ "\n\n/FastQFormat (/q)\n Required for FASTQ input files. Choose from [" + string.Join(",", validFastqFormats) + "]"
+ "\n\n/OutputDirectory:<string> (/o)\n The name of the output directory where all output files will be saved. Relative/Absolute paths are not currently supported."
+ "\n\n/UseExcelHyperlinks (/e)\n Outputs Excel-formatted hyperlinks in the csv file"
+ "\n\n\n*** BLAST Options ***\n"
+ "\n\n/ExecuteBlast (/B)\n Perform a BLAST of the input sequences against a custom database. Windows NCBI BLAST must be installed first"
+ "\n\n/BlastDbPrefix:<string> (/D)\n Database to use for BLAST. The default is UniVec (http://www.ncbi.nlm.nih.gov/VecScreen/UniVec.html)"
+ "\n\n/BlastSize:<int> (/S)\n Limit the number of sequences to be searched by BLAST. Default is " + Resource.BLAST_MAX_SEQUENCES_DEFAULT + "."
;
Console.WriteLine(helpString);
Environment.Exit(-1);
}
// Process all the arguments for correctness
if (!File.Exists(myArgs.InputFile))
{
Console.Error.WriteLine("The file {0} could not be found.", myArgs.InputFile);
Environment.Exit(-1);
}
if (myArgs.OutputDirectory == null)
{
myArgs.OutputDirectory = Path.GetFileNameWithoutExtension(myArgs.InputFile);
}
if (!Directory.Exists(myArgs.OutputDirectory))
{
Directory.CreateDirectory(myArgs.OutputDirectory);
}
if (myArgs.ExecuteBlast)
{
// check to make sure Windows BLAST is installed
if (!BlastLocalHandler.IsLocalBLASTInstalled(BlastLocalHandler.BlastVersion))
{
Console.Error.WriteLine("Unable to find {0} in your PATH environment variable. Please check that BLAST is correctly installed.");
Environment.Exit(-1);
}
if (myArgs.BlastSize < 0)
{
Console.Error.WriteLine("/BlastSize must be greater than 0.");
Environment.Exit(-1);
}
}
return(myArgs);
}