public void TestReadFromMaldiTof()
{
var reader = new MascotGenericFormatReader<Peak>();
List<PeakList<Peak>> pls = reader.ReadFromFile(@"../../../data/pps_192 LC_1141485233.txt");
Assert.AreEqual(81, pls.Count);
Assert.AreEqual(2869.9788, pls[pls.Count - 1].PrecursorMZ);
Assert.AreEqual(0.0, pls[pls.Count - 1].PrecursorIntensity);
Assert.AreEqual(1, pls[pls.Count - 1].PrecursorCharge);
}
public void TestReadFromITMS()
{
var reader = new MascotGenericFormatReader<Peak>();
List<PeakList<Peak>> pls = reader.ReadFromFile(@"../../../data/DHBS0001_4FR_R01.mgf");
Assert.AreEqual(2439, pls.Count);
Assert.AreEqual(1242.05, pls[pls.Count - 1].PrecursorMZ);
Assert.AreEqual(4629, pls[pls.Count - 1].PrecursorIntensity);
Assert.AreEqual(0, pls[pls.Count - 1].PrecursorCharge);
}
public void TestDeduct()
{
var pkls = new MascotGenericFormatReader <Peak>().ReadFromFile(TestContext.CurrentContext.TestDirectory + "/../../../data/TestPeakListDeductionByWindow.mgf");
var pkl = pkls[0];
Assert.AreEqual(296, pkl.Count);
new PeakListDeductionByWindow(6).Deduct(pkl);
Assert.AreEqual(37, pkl.Count);
//pkl.ForEach(m => Console.WriteLine("{0:0.00000}\t{1:0.0}", m.Mz, m.Intensity));
}
public void TestDeduct()
{
var pkls = new MascotGenericFormatReader<Peak>().ReadFromFile(@"../../../data/TestPeakListDeductionByWindow.mgf");
var pkl = pkls[0];
Assert.AreEqual(296, pkl.Count);
new PeakListDeductionByWindow(6).Deduct(pkl);
Assert.AreEqual(37, pkl.Count);
//pkl.ForEach(m => Console.WriteLine("{0:0.00000}\t{1:0.0}", m.Mz, m.Intensity));
}
private static Dictionary <string, PeakList <Peak> > ReadPeakMap(string file, ITitleParser parser)
{
var reader = new MascotGenericFormatReader <Peak>();
List <PeakList <Peak> > hList = reader.ReadFromFile(file);
return(hList.ToDictionary(m =>
{
var filename = parser.GetValue(m.Annotations[MascotGenericFormatConstants.TITLE_TAG] as string);
if (string.IsNullOrEmpty(m.Experimental))
{
m.Experimental = filename.Experimental;
}
if (m.FirstScan == 0)
{
m.FirstScan = filename.FirstScan;
}
if (filename.Charge > 0)
{
m.PrecursorCharge = filename.Charge;
}
return filename.FirstScan.ToString();
}));
}
public override IEnumerable <string> Process(string fileName)
{
var result = new FileInfo(targetDir + "\\" + Path.ChangeExtension(new FileInfo(fileName).Name, ".mgf")).FullName;
int charge = 1;
PeakList <Peak> ms1 = new PeakList <Peak>();
//读取ms1
List <string> comments = new List <string>();
comments.Add("COM=" + software);
using (StreamReader sr = new StreamReader(fileName))
{
string line;
while ((line = sr.ReadLine()) != null)
{
if (line.StartsWith("COM="))
{
comments.Add(line);
continue;
}
if (line.StartsWith("BEGIN IONS"))
{
break;
}
comments.Add(line);
var parts = line.Split('\t');
if (parts.Length == 2)
{
try
{
ms1.Add(new Peak(double.Parse(parts[0]), double.Parse(parts[1])));
}
catch (Exception) { }
}
}
}
MascotGenericFormatReader <Peak> reader = new MascotGenericFormatReader <Peak>();
var pkls = reader.ReadFromFile(fileName);
foreach (var pkl in pkls)
{
var mzTolerance = PrecursorUtils.ppm2mz(pkl.PrecursorMZ, precursorTolerance);
var peak = ms1.FindPeak(pkl.PrecursorMZ, mzTolerance).FindMaxIntensityPeak();
if (peak == null)
{
pkl.PrecursorIntensity = ms1.Min(m => m.Intensity);
}
else
{
pkl.PrecursorIntensity = peak.Intensity;
}
}
pkls.Sort((m1, m2) => m2.PrecursorIntensity.CompareTo(m1.PrecursorIntensity));
for (int i = 0; i < pkls.Count; i++)
{
var line = pkls[i].Annotations[MascotGenericFormatConstants.TITLE_TAG] as string;
var m = reg.Match(line);
string experimental;
if (m.Success)
{
experimental = m.Groups[1].Value;
var m2 = nameReg.Match(experimental);
if (m2.Success)
{
if (m2.Groups[2].Value.Length == 1)
{
experimental = m2.Groups[1].Value + "0" + m2.Groups[2].Value;
}
}
}
else
{
experimental = pkls[i].Experimental;
}
pkls[i].Annotations[MascotGenericFormatConstants.TITLE_TAG] = string.Format("{0}.{1}.{2:0}.{3}.dta", experimental, i + 1, pkls[i].PrecursorIntensity, charge);
}
var writer = new MascotGenericFormatWriter <Peak>();
writer.Comments.AddRange(comments);
writer.WriteToFile(result, pkls);
return(new string[] { result });
}