private void WriteOutputs(string fastaPath, string outputPath)
{
int chromosomeIndex = -1;
using (FastaReader reader = new FastaReader(fastaPath))
using (FastaWriter writer = new FastaWriter(outputPath))
{
GenericRead fastaEntry = new GenericRead();
while (reader.GetNextEntry(ref fastaEntry))
{
chromosomeIndex++;
StringBuilder baseBuilder = new StringBuilder();
BitArray nonUniqueFlags = ChromosomeNonUniqueFlags[chromosomeIndex];
for (int chromPos = 0; chromPos < fastaEntry.Bases.Length; chromPos++)
{
if (nonUniqueFlags[chromPos])
{
baseBuilder.Append(char.ToLowerInvariant(fastaEntry.Bases[chromPos]));
}
else
{
baseBuilder.Append(char.ToUpperInvariant(fastaEntry.Bases[chromPos]));
}
}
writer.WriteEntry(fastaEntry.Name, baseBuilder.ToString());
}
}
}
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 void CreateDatabase()
{
try
{
// Validate Options are kosher
if (Options.InputFiles == null || Options.InputFiles.Count == 0)
{
throw new ArgumentNullException("Input Files");
}
string ext = Path.GetExtension(Options.OutputFastaFile);
if (string.IsNullOrEmpty(ext))
{
ext = ".fasta";
}
string output_filename = Path.GetFullPath(Options.OutputFastaFile);
if (Options.DoNotAppendDatabaseType)
{
output_filename = output_filename + ext;
if (Options.InputFiles.Contains(output_filename))
{
throw new ArgumentException("Output file path cannot be the same as an input file.");
}
}
else
{
switch (Options.OutputType)
{
case DatabaseType.Target:
output_filename += "_TARGET" + ext;
break;
case DatabaseType.Decoy:
output_filename += "_DECOY" + ext;
break;
case DatabaseType.Concatenated:
default:
output_filename += "_CONCAT" + ext;
break;
}
}
string logFilename = Path.GetFileNameWithoutExtension(Options.OutputFastaFile);
string outputFolder = Path.GetDirectoryName(Options.OutputFastaFile);
if (!Directory.Exists(outputFolder))
{
outputFolder = Directory.GetCurrentDirectory();
}
if (Options.GenerateLogFile)
{
switch (Options.OutputType)
{
case DatabaseType.Target:
logFilename += "_TARGET.log";
break;
case DatabaseType.Decoy:
logFilename += "_DECOY.log";
break;
case DatabaseType.Concatenated:
default:
logFilename += "_CONCAT.log";
break;
}
GenerateLog(outputFolder, logFilename);
}
string outputPath = Path.Combine(outputFolder, output_filename);
if (Options.DoNotMergeFiles)
{
foreach (string fastaFile in Options.InputFiles)
{
using (FastaWriter writer = new FastaWriter(outputPath))
{
WriteFasta(fastaFile, writer);
}
}
}
else
{
using (FastaWriter writer = new FastaWriter(outputPath))
{
foreach (string fastaFile in Options.InputFiles)
{
WriteFasta(fastaFile, writer);
}
}
}
if (Options.BlastDatabase)
{
MakeBlastDatabase(outputFolder, output_filename, Path.GetFileNameWithoutExtension(output_filename));
}
}
catch (DirectoryNotFoundException)
{
}
}
