public void WriteFasta(string fasta_file, FastaWriter Writer)
{
bool MakeDecoy = false;
if (Options.OutputType == DatabaseType.Target || Options.OutputType == DatabaseType.Concatenated)
{
MakeDecoy = false;
}
else if (Options.OutputType == DatabaseType.Decoy || Options.OutputType == DatabaseType.Concatenated)
{
MakeDecoy = true;
}
using (FastaReader reader = new FastaReader(fasta_file))
{
foreach (Fasta fasta in reader.ReadNextFasta())
{
Regex uniprotRegex = new Regex(@"(.+)\|(.+)\|(.+?)\s(.+?)\sOS=(.+?)(?:\sGN=(.+?))?(?:$|PE=(\d+)\sSV=(\d+))", RegexOptions.ExplicitCapture);
Match UniprotMatch = uniprotRegex.Match(fasta.Description);
string HeaderFile = "InvalidUniprotheaders.txt";
string headerFolder = Path.GetDirectoryName(Options.InputFiles[0]);
if (Options.EnforceUniprot && !UniprotMatch.Success)
{
using (StreamWriter log = new StreamWriter(Path.Combine(headerFolder, HeaderFile), true))
{
log.WriteLine("Invalid Header:");
log.WriteLine();
log.WriteLine(fasta.Description);
log.WriteLine();
InvalidHeader(fasta);
}
}
if (UniprotMatch.Success)
{
bool excludeMethionine = false;
if (Options.ExcludeNTerminalMethionine && !Options.ExcludeNTerminalResidue)
{
excludeMethionine = true;
}
if (MakeDecoy)
{
Writer.Write(fasta.ToDecoy(Options.DecoyPrefix, Options.DecoyType, (excludeMethionine || Options.ExcludeNTerminalResidue), Options.ExcludeNTerminalMethionine));
}
else
{
Writer.Write(fasta);
}
}
}
}
}
public static Dictionary <string, string> parseDB(string pathIn)
{
Dictionary <string, string> returnDict = new Dictionary <string, string>();
List <string> badsequences = new List <string>();
//StreamReader reader = new StreamReader(pathIn);
var reader = new FastaReader(pathIn);
foreach (var fasta in reader.ReadNextFasta())
{
if (!fasta.IsDecoy)
{
string desc = fasta.Description.Replace(",", ";");
returnDict.Add(">" + desc, fasta.Sequence);
}
}
return(returnDict);
}