/// <summary>
///
/// </summary>
/// <param name="ftp"></param>
/// <param name="dbFilename"></param>
/// <param name="overwrite"></param>
private void GetAndPrepareBlastDB(string ftp, string dbFilename, bool overwrite)
{
Console.Write("Downloading {0} from {0}...", dbFilename, ftp);
var status = BlastLocalHandler.DownloadFasta(ftp, dbFilename, qcm.ContaminationFinder.Blaster.BlastDbPath, overwrite);
Console.WriteLine("status {0}", status);
// FastqFormat FASTA to BLAST database
string fastaFile = qcm.ContaminationFinder.Blaster.BlastDbPath + "/" + dbFilename;
string resultStdOut, resultStdErr;
BlastLocalHandler.MakeBlastDb(fastaFile,
qcm.ContaminationFinder.Blaster.BlastDbPath, "nucl", out resultStdOut, out resultStdErr);
Console.Write(resultStdOut);
Console.Error.Write(resultStdErr);
}
/// <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);
}
