/// <summary>
/// Write the results with the FDR data to the specified file
/// </summary>
/// <param name="outputFilePath"></param>
/// <param name="includeDecoy"></param>
public void WriteTo(string outputFilePath, bool includeDecoy = false)
{
//var resultsToUse = searchResults;
var resultsToUse = filteredResults;
IEnumerable <DatabaseSearchResultData> resultsToWrite;
if (includeDecoy)
{
resultsToWrite = resultsToUse;
}
else
{
resultsToWrite = resultsToUse.Where(x => !x.ProteinName.StartsWith(FastaDatabaseConstants.DecoyProteinPrefix));
}
DatabaseSearchResultData.WriteResultsToFile(outputFilePath, resultsToWrite, true);
}
/// <summary>
/// Read the file at path <paramref name="filePath"/>.
/// </summary>
/// <param name="filePath"></param>
/// <returns></returns>
public static SimpleMZIdentMLReader.SimpleMZIdentMLData ReadResultFile(string filePath)
{
SimpleMZIdentMLReader.SimpleMZIdentMLData results = null;
var lowerFilePath = filePath.ToLower();
if (lowerFilePath.EndsWith(".mzid") || lowerFilePath.EndsWith(".mzid.gz"))
{
var mzidReader = new SimpleMZIdentMLReader();
results = mzidReader.Read(filePath);
}
else if (lowerFilePath.EndsWith("_ictda.tsv"))
{
results = DatabaseSearchResultData.ReadResultsFromFileToMzIdData(filePath);
}
return(results);
}
private bool ReadTargetAndDecoy(string targetResultFilePath, string decoyResultFilePath)
{
var errorBase = "Cannot compute FDR Scores; ";
if (!File.Exists(targetResultFilePath))
{
ErrorMessage = errorBase + "target results file not found, " + Path.GetFileName(targetResultFilePath);
return(false);
}
if (!File.Exists(decoyResultFilePath))
{
ErrorMessage = errorBase + "decoy results file not found, " + Path.GetFileName(decoyResultFilePath);
return(false);
}
var targetData = DatabaseSearchResultData.ReadResultsFromFile(targetResultFilePath);
var decoyData = DatabaseSearchResultData.ReadResultsFromFile(decoyResultFilePath);
return(AddTargetAndDecoyData(targetData, decoyData));
}