public static void TestEverything()
{
Console.WriteLine("UNIT TEST - Entering unit test");
string elements = Path.Combine(TestContext.CurrentContext.TestDirectory, "elements.dat");
string files = TestContext.CurrentContext.TestDirectory;
string ident = Path.Combine(TestContext.CurrentContext.TestDirectory, "aggregatePSMs_5ppmAroundZero.psmtsv");
FlashLFQEngine engine = new FlashLFQEngine();
Console.WriteLine("UNIT TEST - About to load elements");
Loaders.LoadElements(elements);
Console.WriteLine("UNIT TEST - Finished loading elements");
Assert.That(engine.ParseArgs(new string[] {
"--idt " + ident,
"--rep " + files,
"--ppm 5",
"--sil false",
"--pau false",
"--mbr true"
}
));
Console.WriteLine("UNIT TEST - Done making engine");
engine.globalStopwatch.Start();
Assert.That(engine.outputFolder != null);
engine.SetParallelization(1);
//Assert.That(engine.ReadPeriodicTable());
Console.WriteLine("UNIT TEST - About to read TSV file");
Assert.That(engine.ReadIdentificationsFromTSV());
Console.WriteLine("UNIT TEST - Finished reading TSV");
engine.ConstructIndexTemplateFromIdentifications();
Console.WriteLine("UNIT TEST - Finished constructing bins");
Assert.That(engine.observedMzsToUseForIndex.Count > 0);
Assert.That(engine.baseSequenceToIsotopicDistribution.Count > 0);
Console.WriteLine("UNIT TEST - Bins are OK");
for (int i = 0; i < engine.filePaths.Length; i++)
{
Console.WriteLine("UNIT TEST - Quantifying file " + (i + 1));
try
{
Assert.That(engine.Quantify(null, engine.filePaths[i]));
}
catch (AssertionException)
{
Console.WriteLine("UNIT TEST - Could not quantify file \"" + engine.filePaths[i] + "\"");
}
}
//if (engine.mbr)
// engine.RetentionTimeCalibrationAndErrorCheckMatchedFeatures();
Console.WriteLine("UNIT TEST - Quantifying proteins ");
engine.QuantifyProteins();
Console.WriteLine("UNIT TEST - Asserting results");
Assert.That(engine.SumFeatures(engine.allFeaturesByFile.SelectMany(p => p), true).Any());
Assert.That(engine.SumFeatures(engine.allFeaturesByFile.SelectMany(p => p), false).Any());
Assert.That(engine.allFeaturesByFile[0].First().intensity > 0);
Assert.That(engine.allFeaturesByFile[1].First().intensity > 0);
Assert.That(engine.allFeaturesByFile[0].Count == 1);
Assert.That(engine.allFeaturesByFile[1].Count == 1);
Assert.That(!engine.allFeaturesByFile[0].First().isMbrFeature);
Assert.That(!engine.allFeaturesByFile[1].First().isMbrFeature);
Console.WriteLine("UNIT TEST - All passed");
}
public static void TestExternalNoPassedFile()
{
Console.WriteLine("UNIT TEST - Entering unit test");
string[] filePaths = Directory.GetFiles(TestContext.CurrentContext.TestDirectory).Where(f => f.Substring(f.IndexOf('.')).ToUpper().Equals(".RAW") || f.Substring(f.IndexOf('.')).ToUpper().Equals(".MZML")).ToArray();
string elements = Path.Combine(TestContext.CurrentContext.TestDirectory, "elements.dat");
string ident = Path.Combine(TestContext.CurrentContext.TestDirectory, "aggregatePSMs_5ppmAroundZero.psmtsv");
FlashLFQEngine engine = new FlashLFQEngine();
Console.WriteLine("UNIT TEST - About to load elements");
Loaders.LoadElements(elements);
Console.WriteLine("UNIT TEST - Finished loading elements");
engine.PassFilePaths(filePaths);
Assert.That(engine.ParseArgs(new string[] {
"--ppm 5",
"--sil false",
"--pau false",
"--mbr true"
}
));
Console.WriteLine("UNIT TEST - Done making engine");
engine.globalStopwatch.Start();
engine.SetParallelization(1);
Console.WriteLine("UNIT TEST - Adding identifications");
var ids = File.ReadAllLines(ident);
int lineCount = 1;
foreach (var line in ids)
{
if (lineCount != 1)
{
var splitLine = line.Split('\t');
engine.AddIdentification(Path.GetFileNameWithoutExtension(splitLine[0]), splitLine[20], splitLine[21], double.Parse(splitLine[27]), double.Parse(splitLine[2]), (int)double.Parse(splitLine[6]), new List <string> {
splitLine[14]
});
}
lineCount++;
}
Console.WriteLine("UNIT TEST - Finished adding IDs");
engine.ConstructIndexTemplateFromIdentifications();
Console.WriteLine("UNIT TEST - Finished constructing bins");
Assert.That(engine.observedMzsToUseForIndex.Count > 0);
Assert.That(engine.baseSequenceToIsotopicDistribution.Count > 0);
Console.WriteLine("UNIT TEST - Bins are OK");
for (int i = 0; i < engine.filePaths.Length; i++)
{
Console.WriteLine("UNIT TEST - Quantifying file " + (i + 1));
try
{
Assert.That(engine.Quantify(null, engine.filePaths[i]));
}
catch (AssertionException)
{
Console.WriteLine("UNIT TEST - Could not quantify file \"" + engine.filePaths[i] + "\"");
}
}
//if (engine.mbr)
// engine.RetentionTimeCalibrationAndErrorCheckMatchedFeatures();
Console.WriteLine("UNIT TEST - Quantifying proteins ");
engine.QuantifyProteins();
Console.WriteLine("UNIT TEST - Asserting results");
Assert.That(engine.SumFeatures(engine.allFeaturesByFile.SelectMany(p => p), true).Any());
Assert.That(engine.SumFeatures(engine.allFeaturesByFile.SelectMany(p => p), false).Any());
Assert.That(engine.allFeaturesByFile[0].First().intensity > 0);
Assert.That(engine.allFeaturesByFile[1].First().intensity > 0);
Assert.That(!engine.allFeaturesByFile[0].First().isMbrFeature);
Assert.That(!engine.allFeaturesByFile[1].First().isMbrFeature);
Console.WriteLine("UNIT TEST - All passed");
}
static void Main(string[] args)
{
FlashLFQEngine engine = new FlashLFQEngine();
engine.globalStopwatch.Start();
if (!engine.ReadPeriodicTable(null))
{
return;
}
if (!engine.ParseArgs(args))
{
return;
}
if (!engine.ReadIdentificationsFromTSV())
{
return;
}
engine.ConstructIndexTemplateFromIdentifications();
Parallel.For(0, engine.filePaths.Length,
new ParallelOptions {
MaxDegreeOfParallelism = 1
},
fileNumber =>
{
if (!engine.Quantify(null, engine.filePaths[fileNumber]) && !engine.silent)
{
Console.WriteLine("Error quantifying file " + engine.filePaths[fileNumber]);
}
GC.Collect();
}
);
if (engine.mbr)
{
engine.RetentionTimeCalibrationAndErrorCheckMatchedFeatures();
}
if (!engine.WriteResults("_FlashLFQ_", true, true, true))
{
return;
}
if (!engine.silent)
{
Console.WriteLine("All done");
}
if (!engine.silent)
{
Console.WriteLine("Analysis time: " + engine.globalStopwatch.Elapsed.Hours + "h " + engine.globalStopwatch.Elapsed.Minutes + "m " +
engine.globalStopwatch.Elapsed.Seconds + "s");
}
if (engine.pause)
{
Console.ReadKey();
}
}