public static void WriteOutput(string inputPath, FlashLfqResults results, string outputPath = null)
{
if (outputPath == null)
{
outputPath = Path.GetDirectoryName(inputPath);
}
string inputFileName = Path.GetFileNameWithoutExtension(inputPath);
if (!Directory.Exists(outputPath))
{
Directory.CreateDirectory(outputPath);
}
string append = "_FlashLFQ_";
if (inputFileName.ToLowerInvariant().Contains("flashlfq"))
{
append = "_";
}
results.WriteResults(
outputPath + Path.DirectorySeparatorChar + inputFileName + append + "QuantifiedPeaks.tsv",
outputPath + Path.DirectorySeparatorChar + inputFileName + append + "QuantifiedPeptides.tsv",
outputPath + Path.DirectorySeparatorChar + inputFileName + append + "QuantifiedProteins.tsv"
);
}
public static void WriteOutput(string inputPath, FlashLfqResults results, string outputPath = null)
{
if (outputPath == null)
{
outputPath = Path.GetDirectoryName(inputPath);
}
string inputFileName = Path.GetFileNameWithoutExtension(inputPath);
if (!Directory.Exists(outputPath))
{
Directory.CreateDirectory(outputPath);
}
results.WriteResults(
outputPath + Path.DirectorySeparatorChar + inputFileName + "_FlashLFQ_QuantifiedPeaks.tsv",
outputPath + Path.DirectorySeparatorChar + inputFileName + "_FlashLFQ_QuantifiedModifiedSequences.tsv",
outputPath + Path.DirectorySeparatorChar + inputFileName + "_FlashLFQ_QuantifiedBaseSequences.tsv",
outputPath + Path.DirectorySeparatorChar + inputFileName + "_FlashLFQ_QuantifiedProteins.tsv"
);
}
public static void WriteOutput(string inputPath, FlashLfqResults results, bool silent, string outputPath = null)
{
if (outputPath == null)
{
outputPath = Path.GetDirectoryName(inputPath);
}
string inputFileName = Path.GetFileNameWithoutExtension(inputPath);
if (!Directory.Exists(outputPath))
{
Directory.CreateDirectory(outputPath);
}
bool bayesianResults = results.ProteinGroups.Any(p => p.Value.ConditionToQuantificationResults.Any());
results.WriteResults(
Path.Combine(outputPath, "QuantifiedPeaks.tsv"),
Path.Combine(outputPath, "QuantifiedPeptides.tsv"),
Path.Combine(outputPath, "QuantifiedProteins.tsv"),
bayesianResults ? Path.Combine(outputPath, "BayesianFoldChangeAnalysis.tsv") : null,
silent
);
}
