public static void SeparateForwardAndReverse(string fastaFile)
{
try
{
FileStream fs;
try
{
fs = new FileStream(fastaFile, FileMode.Open, FileAccess.Read, FileShare.Read);
}
catch (System.Exception)
{
fs = new FileStream(fastaFile, FileMode.Open, FileAccess.Read, FileShare.ReadWrite);
}
vsCSVWriter wrForward = new vsCSVWriter(vsCSV.GetFolder(fastaFile) + vsCSV.GetFileName_NoExtension(fastaFile) + "_ForwardOnly.fasta");
vsCSVWriter wrReverse = new vsCSVWriter(vsCSV.GetFolder(fastaFile) + vsCSV.GetFileName_NoExtension(fastaFile) + "_ReverseOnly.fasta");
using (StreamReader sr = new StreamReader(fs))
{
ProteinIdType idType = ProteinIdType.Unknown;
string line;
while ((line = sr.ReadLine()) != null)
{
if (line.StartsWith(">"))
{
if (line.StartsWith(">REVERSE_"))
{
idType = ProteinIdType.Reverse;
}
else
{
idType = ProteinIdType.Forward;
}
}
switch (idType)
{
case ProteinIdType.Forward: wrForward.AddLine(line); break;
case ProteinIdType.Reverse: wrReverse.AddLine(line); break;
case ProteinIdType.Unknown: break;
}
}
}
fs.Close();
wrForward.WriteToFile();
wrReverse.WriteToFile();
}
catch (System.Exception ex)
{
Console.WriteLine(ex.Message);
Console.WriteLine(ex.StackTrace);
}
}
public static void ShuffleSequences(string fastaFile)
{
try
{
FileStream fs;
try
{
fs = new FileStream(fastaFile, FileMode.Open, FileAccess.Read, FileShare.Read);
}
catch (System.Exception)
{
fs = new FileStream(fastaFile, FileMode.Open, FileAccess.Read, FileShare.ReadWrite);
}
vsCSVWriter wrShuffled = new vsCSVWriter(vsCSV.GetFolder(fastaFile) + vsCSV.GetFileName_NoExtension(fastaFile) + "_Shuffled.fasta");
using (StreamReader sr = new StreamReader(fs))
{
ProteinIdType idType = ProteinIdType.Unknown;
string line;
string aaSeq = "";
while ((line = sr.ReadLine()) != null)
{
if (line.StartsWith(">"))
{
if (!string.IsNullOrEmpty(aaSeq))
{
wrShuffled.AddLine(Proteomics.Utilities.Tools.AminoAcidTools.Shuffle(aaSeq));
}
wrShuffled.AddLine(line);
aaSeq = "";
}
else
{
aaSeq += line;
}
}
if (!string.IsNullOrEmpty(aaSeq))
{
wrShuffled.AddLine(Proteomics.Utilities.Tools.AminoAcidTools.Shuffle(aaSeq));
}
}
fs.Close();
wrShuffled.WriteToFile();
}
catch (System.Exception ex)
{
Console.WriteLine(ex.Message);
Console.WriteLine(ex.StackTrace);
}
}
public static void MergeSequences(string fastaFolder)
{
try
{
FileStream fsOut = new FileStream(fastaFolder + "merge3.fasta", FileMode.CreateNew);
using (StreamWriter sw = new StreamWriter(fsOut))
{
foreach (string fastaFile in Directory.EnumerateFiles(fastaFolder, "whole_genome.fasta"))
{
FileStream fs;
try
{
fs = new FileStream(fastaFile, FileMode.Open, FileAccess.Read, FileShare.Read);
}
catch (System.Exception)
{
fs = new FileStream(fastaFile, FileMode.Open, FileAccess.Read, FileShare.ReadWrite);
}
using (StreamReader sr = new StreamReader(fs))
{
ProteinIdType idType = ProteinIdType.Unknown;
string line;
while ((line = sr.ReadLine()) != null)
{
if (!string.IsNullOrEmpty(line))
{
sw.WriteLine(line);
}
}
}
fs.Close();
}
}
fsOut.Close();
}
catch (System.Exception ex)
{
Console.WriteLine(ex.Message);
Console.WriteLine(ex.StackTrace);
}
}