private void GCtoCSV_Click(object sender, RoutedEventArgs e)
{
SaveFileDialog saveFileDialog1 = new SaveFileDialog();
saveFileDialog1.InitialDirectory = Project.folderFullPath;
saveFileDialog1.FileName = Project.projectName + "_GC_Content";
saveFileDialog1.Filter = "table (.csv)|*.csv";
if (saveFileDialog1.ShowDialog() == true)
{
if (GCC.generateCSVGc(saveFileDialog1.FileName) == true)
{
MainWindow.main.lblStatus.Content = "Table generated to: " + System.IO.Path.GetFileName(saveFileDialog1.FileName);
}
else
{
MainWindow.main.lblStatus.Content = "Generating GC table failed (No results?).";
Project.ErrorLog.Add("Generating GC table failed (No results?).");
}
}
}
public static bool GenerateCSVTETRA(string file)
{
int computed = Directory.GetFiles(Project.folderFullPath + "\\TETRA\\", "*.tet", SearchOption.TopDirectoryOnly).Length;
if (computed != 0)//make sure there are some results
{
StreamWriter writer = new StreamWriter(file);
writer.Write("name,"); // cell 1:1
string[] tetraPairs = new string[computed];
tetraPairs = Directory.GetFiles(Project.folderFullPath + "\\TETRA\\", "*.tet", SearchOption.TopDirectoryOnly); //array of full filenames
List <string> tetraNames = new List <string>();
foreach (string pair in tetraPairs)
{
tetraNames.Add(Path.GetFileNameWithoutExtension(pair)); //list of filenames without the extensions
}
List <string> tetraNamesUnique = new List <string>();
foreach (string pair in tetraNames)
{
string[] temp = new string[2];
temp = pair.Split(new string[] { "_vs_" }, StringSplitOptions.None);
if (!tetraNamesUnique.Contains(temp[0]))
{
tetraNamesUnique.Add(temp[0]);
}
if (!tetraNamesUnique.Contains(temp[1]))
{
tetraNamesUnique.Add(temp[1]);
}
}//filenames split again to individual fasta names, only unique names matter for the table consturction
foreach (string name in tetraNamesUnique)
{
writer.Write(name + ",");//write first row (fasta names)
}
bool success = false;
foreach (string a in tetraNamesUnique)
{
writer.Write(Environment.NewLine + a + ",");//new row with another name
foreach (string b in tetraNamesUnique)
{
if (a == b)
{
writer.Write("X,"); //this value could also be 100 - comparing the sequence with itself (diagonal)
}
else
{
if (File.Exists(Project.folderFullPath + "\\TETRA\\" + a + "_vs_" + b + ".tet"))
{
StreamReader reader = new StreamReader(Project.folderFullPath + "\\TETRA\\" + a + "_vs_" + b + ".tet");
double GCC;
if (Double.TryParse(reader.ReadLine(), NumberStyles.Any, CultureInfo.InvariantCulture, out GCC))
{
writer.Write(GCC.ToString() + ",");
reader.Close();
success = true;
}
else
{
writer.Write("err,");//error parsing
}
}
else
{
writer.Write("nc,");//not computed
}
}
}
}
writer.Close();
if (success == true) //atleast one valid value in the table
{
return(true);
}
else
{
File.Delete(file); //There is no valid result in the matrix - delete it.
return(false);
}
}
else
{
return(false);
}
}
public static bool GenerateCSVAniAvg(string file)
{
int computed = Directory.GetFiles(Project.folderFullPath + "\\ANI\\", "*.ani", SearchOption.TopDirectoryOnly).Length;
if (computed != 0)//make sure there are some results
{
StreamWriter writer = new StreamWriter(file);
writer.Write("name,"); // cell 1:1
string[] aniPairs = new string[computed];
aniPairs = Directory.GetFiles(Project.folderFullPath + "\\ANI\\", "*.ani", SearchOption.TopDirectoryOnly); //array of full filenames
List<string> aniNames = new List<string>();
foreach (string pair in aniPairs)
{
aniNames.Add(Path.GetFileNameWithoutExtension(pair)); //list of filenames without the extensions
}
List<string> aniNamesUnique = new List<string>();
foreach (string pair in aniPairs)
{
string[] temp = new string[2];
temp = Path.GetFileNameWithoutExtension(pair).Split(new string[] { "_vs_" }, StringSplitOptions.None);
if (!aniNamesUnique.Contains(temp[0])) aniNamesUnique.Add(temp[0]);
if (!aniNamesUnique.Contains(temp[1])) aniNamesUnique.Add(temp[1]);
}//filenames split again to individual fasta names, only unique names matter for the table consturction
foreach (string name in aniNamesUnique)
{
writer.Write(name + ",");//write first row (fasta names)
}
bool success = false;
foreach (string a in aniNamesUnique)
{
writer.Write(Environment.NewLine + a + ",");//new row with another name
foreach (string b in aniNamesUnique)
{
if (a == b)
{
writer.Write("X,"); //A versus A = 100% identity and its pointless to compute or display its result, represented by x
}
else
{
if (File.Exists(Project.folderFullPath + "\\ANI\\" + a + "_vs_" + b + ".ani") && File.Exists(Project.folderFullPath + "\\ANI\\" + b + "_vs_" + a + ".ani"))
{
StreamReader reader1 = new StreamReader(Project.folderFullPath + "\\ANI\\" + a + "_vs_" + b + ".ani");
StreamReader reader2 = new StreamReader(Project.folderFullPath + "\\ANI\\" + b + "_vs_" + a + ".ani");
double GCC1;
double GCC2;
double GCC;
if (Double.TryParse(reader1.ReadLine(), NumberStyles.Any, CultureInfo.InvariantCulture, out GCC1) && Double.TryParse(reader2.ReadLine(), NumberStyles.Any, CultureInfo.InvariantCulture, out GCC2))//verifies valid file structure and content
{
GCC = (GCC1 + GCC2) / 2;
writer.Write(GCC.ToString() + ",");
reader1.Close();
reader2.Close();
success = true;
}
else
{
writer.Write("err,");//error parsing
}
}
else
{
writer.Write("nc,");//not computed
}
}
}
}
writer.Close();
if (success == true) //atleast one valid value in the table
{ return true; }
else
{
File.Delete(file); //There is no valid result in the matrix - delete it.
return false;
}
}
else { return false; }
}
private void GC()
{
int success = 0;
int errors = 0;
if (fastasGC.Count >= 1)
{
foreach (var fasta in fastasGC)
{
if (fasta.GC == true)
{
Status = "Computing GC content " + Path.GetFileNameWithoutExtension(fasta.FullPath);
if (GCC.computeGCcontent(fasta.FullPath) == true)
{
success++;
}
else
{
string error = "File" + System.IO.Path.GetFileNameWithoutExtension(fasta.FullPath) + "no longer exists (it has been deleted, moved or renamed) - removing the file from the project.";
Project.ErrorLog.Add(error);
lblStatusGC.Content = error;
Project.fastas.Remove(fasta.FullPath);
errors++;
}
}
}
}
else
{
string error = "Atleast one valid fasta file must be loaded to compute GC content.";
MessageBox.Show(error, "Warning", MessageBoxButton.OK, MessageBoxImage.Warning);
Status = error;
}
if (errors != 0 && success > 0)
{
string inf = "GC content finished but some files were missing or not accessible, these files were removed from the project.";
MessageBox.Show(inf, "Warning", MessageBoxButton.OK, MessageBoxImage.Warning);
Status = inf;
MainWindow.main.Status = inf;
MainWindow.main.EnableMatrixC();
}
else if (errors == 0 && success > 0)
{
string inf = "Computation finished successfully";
MessageBox.Show(inf, "Sucess", MessageBoxButton.OK, MessageBoxImage.Information);
Status = inf;
MainWindow.main.Status = inf;
MainWindow.main.EnableMatrixC();
}
else
{
string error = "GC conent computation failed for all pairs. Missing files and respective pairs have been removed from the project. For more informations check logs.";
MessageBox.Show(error, "Error", MessageBoxButton.OK, MessageBoxImage.Warning);
Status = error;
MainWindow.main.Status = error;
Project.ErrorLog.Add(error);
}
}
