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; }
}
