private void btnAddFasta_Click(object sender, EventArgs e)
{
DialogResult result = openFastaFileDialog.ShowDialog();
if (result == System.Windows.Forms.DialogResult.OK)
{
PartDetail part = new PartDetail();
//Get the path of specified file
part.PartPath = openFastaFileDialog.FileName;
//Read the contents of the file into a stream
var fileStream = openFastaFileDialog.OpenFile();
using (StreamReader reader = new StreamReader(fileStream))
{
part.FASTAFormat = reader.ReadToEnd();
}
DataRow newRow = dtParts.NewRow();
string sPartName = openFastaFileDialog.SafeFileName.Split('.')[0];
newRow["Part Name"] = sPartName;
part.PartName = sPartName;
newRow["Status"] = "Tests pending...";
dtParts.Rows.Add(newRow);
dicPartDetail.Add(sPartName, part);
dgvParts.DataSource = dtParts;
if (dtParts.Rows.Count == 1)
{
dgvParts.Rows[0].Selected = true;
}
}
}
private void btnTestPart_Click(object sender, EventArgs e)
{
if (txtBlastPath.Text == "" || txtDbPath.Text == "" || txtViennaPath.Text == "")
{
return;
}
if (dtParts.Rows.Count > 0)
{
Cursor.Current = Cursors.WaitCursor;
string selectedPartName = dgvParts.SelectedRows[0].Cells["Part Name"].Value.ToString();
int selectedPartIndex = dgvParts.SelectedRows[0].Index;
PartDetail part = dicPartDetail[selectedPartName];
//Reset status
dtParts.Rows[selectedPartIndex]["Status"] = "Tests pending...";
part.bBlastSuccess = false;
part.bFoldSuccess = false;
//BLAST Process
Process proc1 = new Process();
proc1.StartInfo.WorkingDirectory = Directory.GetCurrentDirectory();
proc1.StartInfo.FileName = txtBlastPath.Text;
proc1.StartInfo.Arguments = "-query " + part.PartPath + " -db " + txtDbPath.Text.Split('.')[0] + " -out " + part.PartName + ".txt -evalue 1e-3 -num_threads 5";
proc1.StartInfo.UseShellExecute = false;
proc1.StartInfo.RedirectStandardError = true;
proc1.StartInfo.RedirectStandardOutput = true;
if (!proc1.Start())
{
MessageBox.Show("Please check that the blastn path is correct.");
return;
}
proc1.WaitForExit();
proc1.Close();
string blastout = File.ReadAllText(part.PartName + ".txt", Encoding.UTF8);
if (blastout.Contains("***** No hits found *****"))
{
part.bBlastSuccess = true;
}
//RNAfold Process
Process proc2 = new Process();
proc2.StartInfo.WorkingDirectory = Directory.GetCurrentDirectory();
proc2.StartInfo.FileName = txtViennaPath.Text;
proc2.StartInfo.Arguments = "-i " + part.PartPath + " -o";
proc2.StartInfo.UseShellExecute = false;
proc2.StartInfo.RedirectStandardError = true;
proc2.StartInfo.RedirectStandardOutput = true;
if (!proc2.Start())
{
MessageBox.Show("Please check that the RNAfold path is correct.");
return;
}
proc2.WaitForExit();
proc2.Close();
string foldout = File.ReadAllText(part.PartName + ".fold", Encoding.UTF8);
if (foldout.Contains("( 0.00)"))
{
part.bFoldSuccess = true;
}
//Report results under status
if (part.bFoldSuccess && part.bBlastSuccess)
{
dtParts.Rows[selectedPartIndex]["Status"] = "Tests Successful";
}
else if (!part.bFoldSuccess && part.bBlastSuccess)
{
dtParts.Rows[selectedPartIndex]["Status"] = "Blast test successful, Fold test failed";
}
else if (!part.bFoldSuccess && !part.bBlastSuccess)
{
dtParts.Rows[selectedPartIndex]["Status"] = "Tests failed";
}
else if (part.bFoldSuccess && !part.bBlastSuccess)
{
dtParts.Rows[selectedPartIndex]["Status"] = "Blast test failed, Fold test successful";
}
}
Cursor.Current = Cursors.Default;
}
