static void Wiff2()
{
string wiffPath = @"C:\Users\david\Documents\BioInfo\47_praktikum\data\task7.wiff";
string runID = "sample=0";
System.Diagnostics.Stopwatch time = new System.Diagnostics.Stopwatch();
time.Start();
Console.Out.WriteLine(time.Elapsed.TotalMinutes);
using (var reader = new WiffFileReader(wiffPath))
using (ITransactionScope txn = reader.BeginTransaction())
{
System.Collections.Generic.IEnumerable <string> Items()
{
foreach (var ms in reader.ReadMassSpectra(runID))
{
//var peaks = reader.ReadSpectrumPeaks(ms.ID);
yield return(ms.ID);
}
}
txn.Commit();
Console.Out.WriteLine(Items().ToArray().Length);
Console.Out.WriteLine(time.Elapsed.TotalMinutes);
}
}
static void WiffToMzML()
{
string wiffPath = @"C:\Work\primaqdev\testdata\C2 Sol SWATH4.wiff";
string runID = "sample=0";
string mzMLOutPath = @"C:\Work\primaqdev\testdata\test.mzML";
using (var wiff = new WiffFileReader(wiffPath))
using (ITransactionScope txn = wiff.BeginTransaction())
using (var mzML = new MzMLWriter(mzMLOutPath))
{
mzML.BeginMzML(wiff.Model);
mzML.BeginRun(wiff.Model.Runs[runID]);
var spectra = wiff.ReadMassSpectra(runID).Take(1);
int spectrumCount = spectra.Count();
int specIdx = 0;
mzML.BeginSpectrumList(spectrumCount);
foreach (var ms in spectra)
{
var bd = wiff.ReadSpectrumPeaks(ms.ID);
mzML.WriteSpectrum(ms, bd, specIdx);
specIdx++;
}
mzML.EndSpectrumList();
mzML.EndRun();
mzML.EndMzML();
mzML.Close();
}
}
static void WiffToSQLite()
{
string wiffPath = @"C:\Work\primaqdev\testdata\C2 Sol SWATH4.wiff";
string mzLitePath = Path.Combine(Path.GetDirectoryName(wiffPath), Path.GetFileNameWithoutExtension(wiffPath) + ".mzlite");
string runID = "sample=0";
if (File.Exists(mzLitePath))
{
File.Delete(mzLitePath);
}
using (IMzLiteDataReader reader = new WiffFileReader(wiffPath))
using (ITransactionScope inTxn = reader.BeginTransaction())
using (MzLiteSQL writer = new MzLiteSQL(mzLitePath))
using (ITransactionScope outTxn = writer.BeginTransaction())
{
foreach (var ms in reader.ReadMassSpectra(runID))
{
var peaks = reader.ReadSpectrumPeaks(ms.ID);
var clonedMS = MzLiteJson.JsonCloneModelItem("#1", ms);
writer.Insert(runID, clonedMS, peaks);
break;
}
foreach (var ms in writer.ReadMassSpectra(runID))
{
var peaks = writer.ReadSpectrumPeaks(ms.ID);
var ms1 = writer.ReadMassSpectrum(ms.ID);
break;
}
outTxn.Commit();
}
}
static void Wiff()
{
string wiffPath = @"C:\Work\primaqdev\testdata\C2 Sol SWATH4.wiff";
string runID = "sample=0";
using (var reader = new WiffFileReader(wiffPath))
{
SWATHIndexer idx = SWATHIndexer.Build(reader, runID);
var ids = idx.Find(558.3, 23.8, 1);
}
}
static void Wiff()
{
string wiffPath = @"C:\Users\david\Documents\BioInfo\47_praktikum\data\task7.wiff";
string runID = "sample=0";
using (var reader = new WiffFileReader(wiffPath))
using (ITransactionScope txn = reader.BeginTransaction())
{
foreach (var ms in reader.ReadMassSpectra(runID))
{
//var peaks = reader.ReadSpectrumPeaks(ms.ID);
Console.Out.WriteLine(ms.ID);
}
}
}
static void WiffToSQLite()
{
string wiffPath = @"C:\Work\primaqdev\testdata\Für Alex\20160212_MS_DHpsan006.wiff";
string mzLitePath = Path.Combine(Path.GetDirectoryName(wiffPath), Path.GetFileNameWithoutExtension(wiffPath) + ".mzlite");
string runID = "sample=0";
int msLevel;
if (File.Exists(mzLitePath))
{
File.Delete(mzLitePath);
}
using (IMzLiteDataReader reader = new WiffFileReader(wiffPath))
using (ITransactionScope inTxn = reader.BeginTransaction())
using (MzLiteSQL writer = new MzLiteSQL(mzLitePath))
using (ITransactionScope outTxn = writer.BeginTransaction())
{
foreach (var ms in reader.ReadMassSpectra(runID))
{
if (ms.TryGetMsLevel(out msLevel) && msLevel != 1)
{
continue;
}
var peaks = reader.ReadSpectrumPeaks(ms.ID);
//var clonedMS = MzLiteJson.JsonCloneModelItem("#1", ms);
//var max = peaks.Peaks.GroupBy(x => x.Intensity);
writer.Insert(runID, ms, peaks);
//break;
}
//foreach (var ms in writer.ReadMassSpectra(runID))
//{
// var peaks = writer.ReadSpectrumPeaks(ms.ID);
// var ms1 = writer.ReadMassSpectrum(ms.ID);
// break;
//}
outTxn.Commit();
}
}
static void TestRt()
{
string wiffPath = @"C:\Work\primaqdev\testdata\swathtest\20141201_BASF5_1SW01.wiff";
string runID = "sample=0";
using (var reader = new WiffFileReader(wiffPath))
using (ITransactionScope txn = reader.BeginTransaction())
{
var rti = reader.BuildRtIndex(runID);
var rtQuery = new RangeQuery(56.8867263793945, 10.0);
var mzQueries = new RangeQuery[]
{
new RangeQuery(890.4764, 0.01),
new RangeQuery(677.3651, 0.01),
new RangeQuery(989.5448, 0.01),
new RangeQuery(776.4335, 0.01)
};
var profile = reader.RtProfiles(rti, rtQuery, mzQueries);
var profil = reader.RtProfile(rti, rtQuery, new RangeQuery(776.4335, 0.01));
}
}
static void TestSwath()
{
string wiffPath = @"C:\Work\primaqdev\testdata\swathtest\20141201_BASF5_1SW01.wiff";
string searchListPath = @"C:\Work\primaqdev\testdata\swathtest\result_N14 - Ions.txt";
string runID = "sample=0";
using (var reader = new WiffFileReader(wiffPath))
using (ITransactionScope txn = reader.BeginTransaction())
using (var csv = CSVReader.GetTabReader(searchListPath))
{
var swath = SwathIndexer.Create(reader, runID);
var queuries = csv.ReadAll()
.GroupBy(x => x.GetDouble("Precursor MZ"))
.Select(x => CreateSwathQuery(x, 1.0, 0.05))
.ToArray();
SwathQuerySorting.Sort(queuries);
Stopwatch stopwatch = new Stopwatch();
stopwatch.Start();
for (int i = 0; i < queuries.Length; i++)
{
if (i % 10 == 0)
{
Console.WriteLine(i);
}
var ms2 = swath.GetMS2(reader, queuries[i]);
}
stopwatch.Stop();
Console.WriteLine("Elapsed time: {0}", stopwatch.Elapsed.ToString());
Console.WriteLine("Press any key to exit.");
System.Console.ReadKey();
}
}
