public void Test()
{
string file = @TestContext.CurrentContext.TestDirectory + "/../../../data//massprofiler.xls";
file = new FileInfo(file).FullName;
PrecursorItemListExcelReader reader = new PrecursorItemListExcelReader();
var list = reader.ReadFromFile(file);
Assert.AreEqual(162, list.Count);
Assert.AreEqual(4.869, list[0].RetentionTime, 0.000);
Assert.AreEqual(1019.4944, list[0].Mz, 0.0000);
Assert.AreEqual(37842.86, list[0].Abundance, 0.00);
}
public static void ProcessConfiguration(PrecursorReproducibitityConfiguration conf, string resultFileName)
{
List <PrecursorItemList> items = new List <PrecursorItemList>();
var reader = new PrecursorItemListExcelReader();
foreach (var file in conf.FileNames)
{
items.Add(reader.ReadFromFile(file));
}
items.ForEach(m => m.Sort((n1, n2) => - n1.Abundance.CompareTo(n2.Abundance)));
using (StreamWriter sw = new StreamWriter(resultFileName))
{
for (int i = 0; i < items.Count; i++)
{
var itemI = items[i];
var fileI = new FileInfo(conf.FileNames[i]).Name;
itemI.ForEach(m => m.Matched = false);
for (int j = i + 1; j < items.Count; j++)
{
var itemJ = items[j];
var fileJ = new FileInfo(conf.FileNames[j]).Name;
itemJ.ForEach(m => m.Matched = false);
List <PairItem> unions = new List <PairItem>();
foreach (var m in itemI)
{
var matched = (from n in itemJ
where (!n.Matched) && (PrecursorUtils.mz2ppm(m.Mz, Math.Abs(m.Mz - n.Mz)) < conf.PPMTolerance)
select n).ToList();
if (matched.Count > 0)
{
matched.Sort((m1, m2) => Math.Abs(m1.RetentionTime - m.RetentionTime).CompareTo(Math.Abs(m2.RetentionTime - m.RetentionTime)));
matched[0].Matched = true;
m.Matched = true;
unions.Add(new PairItem()
{
Item1 = m,
Item2 = matched[0],
Used = false
});
}
}
var rts = (from u in unions
orderby u.RetentionTimeDiff
select u).ToList();
//keep 90% to do statistic.
int count = rts.Count / 20;
rts = rts.Take(rts.Count - count).Skip(count).ToList();
rts.ForEach(m => m.Used = true);
sw.WriteLine("{0} vs {1}\tmatched {2}", fileI, fileJ, rts.Count);
var acc = new MeanStandardDeviation(rts.ConvertAll(m => m.RetentionTimeDiff).ToArray());
sw.WriteLine("RETENTION TIME : Mean = {0:0.0000}, SD = {1:0.0000}", acc.Mean, acc.StdDev);
var abundances = from u in unions
select u.AbundanceDiff;
acc = new MeanStandardDeviation(abundances.ToArray());
sw.WriteLine("ABUNDANCE : Mean = {0:0.0000}, SD = {1:0.0000}", acc.Mean, acc.StdDev);
sw.WriteLine("MZ\tRT1\tRT2\tABUNDANCE1\tABUNDANCE2\tRTDiff\tAbundanceDiff\tUsed");
unions.Sort((m1, m2) => m1.Mz.CompareTo(m2.Mz));
unions.ForEach(m => sw.WriteLine("{0:0.0000}\t{1:0.0000}\t{2:0.0000}\t{3:0.0000}\t{4:0.0000}\t{5:0.0000}\t{6:0.0000}\t{7}",
m.Mz,
m.Item1.RetentionTime,
m.Item2.RetentionTime,
m.Item1.Abundance,
m.Item2.Abundance,
m.RetentionTimeDiff,
m.AbundanceDiff,
m.Used));
WriteOnlyItem(sw, itemI, fileI + " only");
WriteOnlyItem(sw, itemJ, fileJ + " only");
}
}
}
}
