public void filterTaggedSeqFile()
{
using (StreamReader snpTagReader = File.OpenText(filePath))
{
string line;
string outputFile = folderPath + "\\filteredSnpTaggedSeqs.txt";
FileVerifier fv = new FileVerifier();
int verified = fv.verifyFileExistence(outputFile, " filtered sequence file ", folderPath, formObj);
if (verified == 1)
{
Stream stream = null;
try
{
stream = new FileStream(outputFile, FileMode.Append, FileAccess.Write);
using (StreamWriter sw = new StreamWriter(stream))
{
while ((line = snpTagReader.ReadLine()) != null)
{
string[] items = line.Split('\t');
int snpCnt = int.Parse(items[1]); // Total snps in transcript
if (snpCnt >= snpMin)
{
stream = null;
sw.WriteLine(line);
}
}
}
}
finally
{
if (stream != null)
{
stream.Dispose();
}
}
}
}
}
/*****************************************************
* Event handler for calculating snp frequencies
*****************************************************/
/// <summary>
/// Event-handler that generates a snp-tagged sequence,
/// i.e., a sequence of "x" and "s" characters, where
/// "s" represents the presence of a snp at a specific
/// index in the "x" string
/// </summary>
/// <param name="sender"></param>
/// <param name="e"></param>
private void createTaggedSeqButton_Click(object sender, EventArgs e)
{
// First do some validation (no field can be empty)
foreach (Control control in ActiveForm.Controls)
{
string controlType = control.GetType().ToString();
if (controlType == "System.Windows.Forms.TextBox")
{
TextBox txtBox = (TextBox)control;
if (string.IsNullOrEmpty(txtBox.Text))
{
MessageBox.Show("All fields must be filled.");
txtBox.Focus();
return;
}
}
}
// Add the contents of the snps loci file to an array
/****************************************************/
try
{
outF = this.outputFolderTextBox.Text;
string pathResultFile = outF + "\\snpTaggedSeqs.txt";
FileVerifier fv = new FileVerifier();
int verified = fv.verifyFileExistence(pathResultFile, " masked sequence file ", outF, this);
if (verified == 1)
{
try
{
int[][] snps = (from line in File.ReadAllLines(snpFileTextBox.Text)
select(from item in line.Split('\t')
select int.Parse(item)).ToArray()).ToArray();
// Call method that will mark snps in seqs
string seqF = this.seqFileTextBox.Text;
SeqMasker sm = new SeqMasker(seqF, outF);
Stopwatch sw = new Stopwatch();
sw.Start();
Cursor.Current = Cursors.WaitCursor;
sm.tagSnpsOnSeqs(snps);
Cursor.Current = Cursors.Default;
sw.Stop();
MessageBox.Show("Finished Creating Masked Sequences! It took " + sw.Elapsed + Environment.NewLine + "Now filtering ...", "Completed Phase 1");
}
catch
{
MessageBox.Show("Please, make sure that your snp file includes only integers as chromosome names.\n" +
"In case you have chromosome names with strings, replace those with integers.\n" +
"This includes chromosomes X and Y.", "Error reading snp file", MessageBoxButtons.OK, MessageBoxIcon.Stop);
}
}
}
catch
{
MessageBox.Show("Possible issue with the path to output folder; please verify that you have entered the complete plath.",
"Error reading snp file", MessageBoxButtons.OK, MessageBoxIcon.Stop);
}
}