/// <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 a FASTA file to a BLAST database
/// </summary>
/// <param name="fastaFile">Input FASTA file</param>
/// <param name="blastDbPath">Path of BLAST db directory</param>
/// <param name="molecularType">Molecular type of input</param>
/// <param name="resultStdOut">Store standard output text from the process</param>
/// <param name="resultStdErr">Store standard error text from the process</param>
static public void MakeBlastDb(string fastaFile, string blastDbPath, string molecularType, out string resultStdOut, out string resultStdErr)
{
if (!File.Exists(fastaFile))
{
throw new ArgumentNullException("fastaFile");
}
// Molecular type can only be 'nucl' or 'prot'
if (!(molecularType == "nucl" || molecularType == "prot"))
{
throw new ArgumentException("Invalid BLAST argument: molecular type " + molecularType
+ " not recognized");
}
// Set up parameters
string dbName = Path.GetFileNameWithoutExtension(fastaFile);
string exe = "makeblastdb";
string commandArguments = "-in " + BlastTools.InDoubleQuotes(dbName)
+ " -out " + BlastTools.InDoubleQuotes(dbName)
+ " -dbtype " + molecularType
;
// Temporarily change working directory to blastdb.
// This is because makeblastdb wasn't playing nice with
// arguments that have spaces within.
var oldWorkingDirectory = Directory.GetCurrentDirectory();
Directory.SetCurrentDirectory(blastDbPath);
// Start the process
ProcessStartInfo psi = new ProcessStartInfo
{
FileName = exe,
Arguments = commandArguments,
UseShellExecute = false,
RedirectStandardOutput = true,
RedirectStandardError = true
};
using (Process p = Process.Start(psi))
{
using (StreamReader reader = p.StandardOutput)
{
resultStdOut = reader.ReadToEnd();
//Console.Write(result);
}
using (StreamReader error = p.StandardError)
{
resultStdErr = error.ReadToEnd();
//Console.Error(resultError);
}
}
// Change back to previous directory
Directory.SetCurrentDirectory(oldWorkingDirectory);
}
