static int DoStuff(ArgumentParser.QcOptions opts)
{
Log.Information("Starting QC. Identipy: {Identipy}", opts.Identipy);
//Console.WriteLine("\n");
/*
* if (new List<string>() { "DDA", "DIA", "PRM" }.Contains(opts.ExperimentType))
* { }
* else
* {
* Log.Error("Experiment type of {ExpType} was passed", opts.ExperimentType);
* Console.WriteLine("Experiment type must be one of ['DDA', 'DIA', 'PRM'], not {0}", opts.ExperimentType);
* Environment.Exit(1);
* }*/
if (opts.SearchAlgorithm != null & !(new List <string>()
{
"identipy", "xtandem", "None"
}.Contains(opts.SearchAlgorithm)))
{
// the search algorithm is not null but it also it not identipy or xtandem
Log.Error("Invalid search algorithm argument: {Argument}", opts.SearchAlgorithm);
Console.WriteLine("ERROR: Search algorithm must be one of {identipy, xtandem}");
return(1);
}
if (opts.Identipy)
{
opts.SearchAlgorithm = "identipy";
}
WorkflowParameters parameters = new WorkflowParameters(opts);
if (opts.SearchAlgorithm != "None")
{
if (opts.FastaDatabase == null)
{
Log.Error("No fasta database provided for Identipy search");
Console.WriteLine("ERROR: A fasta protein database is required for a database search. Please use the --db parameter to " +
"provide the path to a database.");
Environment.Exit(1);
}
if (opts.SearchAlgorithm == "identipy")
{
if ((opts.IdentipyScript == null & opts.PythonExecutable != null) | (opts.IdentipyScript != null & opts.PythonExecutable == null))
{
Log.Error("If providing location of python or identipy, must specify both of them.");
Console.WriteLine("ERROR: When invoking the -p or -I options, you must supply both of them.");
Environment.Exit(1);
}
Identipy.CheckIdentipyDependencies(parameters);
}
if (opts.SearchAlgorithm == "xtandem")
{
if (opts.XTandemDirectory == null)
{
Log.Error("Path to XTandem directory was not provided");
Console.WriteLine("ERROR: You must specify the X! Tandem directory using the -X argument to perform a search using X! Tandem.");
return(1);
}
}
}
QC.QcWorkflow.DoQc(parameters, opts.SubdirectoriesIncluded);
return(0);
}
static int DoStuff(ArgumentParser.QcOptions opts)
{
Log.Information("Starting QC. Identipy: {Identipy}", opts.Identipy);
//Console.WriteLine("\n");
SearchParameters searchParameters;
QcParameters qcParameters = new QcParameters();
qcParameters.RawFileDirectory = opts.DirectoryToQc;
qcParameters.QcDirectory = opts.QcDirectory;
qcParameters.QcFile = Path.Combine(opts.QcDirectory, "QC.xml");
if (opts.SearchAlgorithm != null & !(new List <string>()
{
"identipy", "xtandem"
}.Contains(opts.SearchAlgorithm)))
{
// the search algorithm is not null but it also it not identipy or xtandem
Log.Error("Invalid search algorithm argument: {Argument}", opts.SearchAlgorithm);
Console.WriteLine("ERROR: Search algorithm must be one of {identipy, xtandem}");
return(1);
}
if (opts.Identipy)
{
opts.SearchAlgorithm = "identipy";
}
if (opts.SearchAlgorithm != null)
{
if (opts.FastaDatabase == null)
{
Log.Error("No fasta database provided for Identipy search");
Console.WriteLine("ERROR: A fasta protein database is required for an Identipy search. Please use the --db parameter to " +
"provide the path to a database.");
Environment.Exit(1);
}
searchParameters = new SearchParameters
{
PythonExecutable = opts.PythonExecutable,
IdentipyScript = opts.IdentipyScript,
XTandemDirectory = opts.XTandemDirectory,
FastaDatabase = opts.FastaDatabase,
FixedMods = opts.FixedMods,
NMod = opts.VariableNMod,
KMod = opts.VariableKMod,
XMod = opts.VariableXMod,
NumSpectra = opts.NumberSpectra,
MgfIntensityCutoff = opts.IntensityCutoff,
MgfMassCutoff = opts.MassCutOff,
FixedScans = opts.FixedScans
};
if (opts.SearchAlgorithm == "identipy")
{
if ((opts.IdentipyScript == null & opts.PythonExecutable != null) | (opts.IdentipyScript != null & opts.PythonExecutable == null))
{
Log.Error("If providing location of python or identipy, must specify both of them.");
Console.WriteLine("ERROR: When invoking the -p or -I options, you must supply both of them.");
Environment.Exit(1);
}
Identipy.CheckIdentipyDependencies(searchParameters);
searchParameters.SearchAlgorithm = SearchAlgorithm.IdentiPy;
}
if (opts.SearchAlgorithm == "xtandem")
{
if (opts.XTandemDirectory == null)
{
Log.Error("Path to XTandem directory was not provided");
Console.WriteLine("ERROR: You must specify the X! Tandem directory using the -X argument to perform a search using X! Tandem.");
return(1);
}
searchParameters.SearchAlgorithm = SearchAlgorithm.XTandem;
}
}
else
{
searchParameters = null;
}
qcParameters.searchParameters = searchParameters;
QC.QC.DoQc(qcParameters);
return(0);
}