public void RunProteinAnalysis()
{
List <ProteinAnalysis> myAnalysis = new List <ProteinAnalysis>();
foreach (FastaItem fi in core.MyFastaItems)
{
//Get the related peptides
List <PeptideAnalysis> myPeps = (from pa in MyPeptideAnalyses.AsParallel()
where fi.Sequence.Contains(PatternTools.pTools.CleanPeptide(pa.Sequence, true))
select pa).ToList();
List <string> cleanedPeps = myPeps.Select(a => a.Sequence).Distinct().ToList();
double cov = fi.Coverage(cleanedPeps, true);
ProteinAnalysis pepAnalysis = new ProteinAnalysis(fi, cov, myPeps);
myAnalysis.Add(pepAnalysis);
}
MyProteinAnalyses = myAnalysis;
}
public void RunPeptideAnalysis(bool normalizeTIC, List <int> acceptableClasses, bool onlyUniquePeptides, int minMS1Count, double minFold)
{
NormalizeTIC = normalizeTIC;
AcceptableClasses = acceptableClasses;
OnlyUniquePeptides = onlyUniquePeptides;
MinMS1Count = minMS1Count;
MinFold = minFold;
if (AcceptableClasses.Count != 2)
{
throw new Exception("Please input 2 classes for peptide analysis");
}
if (normalizeTIC && !wasNormalized)
{
Console.WriteLine("Normalizing");
wasNormalized = true;
foreach (QuantPackage2 qp in core.myQuantPkgs)
{
double tic = (from file in qp.MyQuants
from q in file.Value
select q.QuantArea).Sum();
foreach (List <Quant> peptide in qp.MyQuants.Values)
{
foreach (Quant quan in peptide)
{
quan.QuantArea /= tic;
}
}
}
}
List <string> peptides = (from qp in core.myQuantPkgs
where AcceptableClasses.Contains(qp.ClassLabel)
from peptide in qp.MyQuants
from quan in peptide.Value
select peptide.Key + "::" + quan.Z).OrderBy(a => a).Distinct().ToList();
//First we will get the scan numbers and then retrieve them from the sepro package
List <AssociationItem> pairs = core.MyAssociationItems.FindAll(a => AcceptableClasses.Contains(a.Label));
pairs.Sort((a, b) => a.Label.CompareTo(b.Label));
//Build the matrix
Console.WriteLine("Mounting peptide matrix");
List <int> associations = pairs.Select(a => a.Assosication).Distinct().ToList();
associations.Sort();
ConcurrentBag <PeptideAnalysis> myPepAnalysis = new ConcurrentBag <PeptideAnalysis>();
int counter = 0;
int ZeroCounter = 0;
int PlusCounter = 0;
int MinusCounter = 0;
int PositiveRatio = 0;
int NegativeRatio = 0;
//Parallel.For(0, peptides.Count, y =>
for (int y = 0; y < peptides.Count; y++)
{
string[] cols = Regex.Split(peptides[y], "::");
string pepSeq = cols[0];
int z = int.Parse(cols[1]);
string[] associationResults = new string[associations.Count];
int noPtns = core.PeptideProteinDictionary[PatternTools.pTools.CleanPeptide(pepSeq, true)].Count;
if (onlyUniquePeptides && noPtns == 1 || !onlyUniquePeptides)
{
//var qs = (from qp in core.myQuantPkgs
// where AcceptableClasses.Contains(qp.ClassLabel)
// from peptide in qp.MyQuants.AsParallel()
// from quan in peptide.Value
// where peptide.Key.Equals(pepSeq) && quan.Z == z
// select new { File = qp.FileName, Q = quan }).ToList();
for (int x = 0; x < associations.Count; x++)
{
List <AssociationItem> myAss = pairs.FindAll(a => a.Assosication == associations[x]);
//List<Quant> q1 = qs.FindAll(a => a.File.Equals(myAss[0].FileName)).Select(b => b.Q).ToList();
//List<Quant> q2 = qs.FindAll(a => a.File.Equals(myAss[1].FileName)).Select(b => b.Q).ToList();
List <Quant> q1 = (from qp in core.myQuantPkgs
where qp.FileName.Equals(myAss[0].FileName) && AcceptableClasses.Contains(qp.ClassLabel)
from peptide in qp.MyQuants
from quan in peptide.Value
where peptide.Key.Equals(pepSeq) && quan.Z == z
select quan).ToList();
List <Quant> q2 = (from qp in core.myQuantPkgs
where qp.FileName.Equals(myAss[1].FileName) && AcceptableClasses.Contains(qp.ClassLabel)
from peptide in qp.MyQuants
from quan in peptide.Value
where peptide.Key.Equals(pepSeq) && quan.Z == z
select quan).ToList();
double v1 = -1;
double v2 = -1;
if (q1.Count > 0)
{
if (q1[0].MyIons.GetLength(1) < minMS1Count)
{
v1 = 0;
}
else if (q1[0].QuantArea > 0)
{
v1 = q1[0].QuantArea;
}
}
if (q2.Count > 0)
{
if (q2[0].MyIons.GetLength(1) < minMS1Count)
{
v2 = 0;
}
else if (q2[0].QuantArea > 0)
{
v2 = q2[0].QuantArea;
}
}
if (q1.Count <= 0 && q2.Count <= 0)
{
associationResults[x] = "0";
}
else if (v1 > 0 && v2 > 0)
{
if (((v1 / v2) < minFold) && ((v2 / v1) < minFold))
{
associationResults[x] = "0";
ZeroCounter++;
}
else
{
double ratio = (v1 / v2);
associationResults[x] = ratio.ToString();
if (ratio >= 1)
{
PositiveRatio++;
}
else
{
NegativeRatio++;
}
}
}
else if (v1 > 0 && v2 <= 0)
{
associationResults[x] = "+";
PlusCounter++;
}
else if (v1 <= 0 && v2 > 0)
{
associationResults[x] = "-";
MinusCounter++;
}
else if ((v1 == -1 && v2 == 0) || (v2 == -1 && v1 == 0) || (v1 == 0 && v2 == 0))
{
associationResults[x] = "0";
ZeroCounter++;
}
else
{
Console.WriteLine("We Shouldn't be here");
}
}
PeptideAnalysis thisPep = new PeptideAnalysis(pepSeq, z, associationResults);
if (noPtns == 1)
{
thisPep.IsUnique = true;
}
else
{
thisPep.IsUnique = false;
}
myPepAnalysis.Add(thisPep);
Console.Write("\r{0} / {1} ", ++counter, peptides.Count);
}
}
//);
MyPeptideAnalyses = myPepAnalysis.ToList();
MyPeptideAnalyses.Sort((a, b) => a.Sequence.CompareTo(b.Sequence));
Console.WriteLine("Counter = " + counter);
Console.WriteLine("Zero Counter = " + ZeroCounter);
Console.WriteLine("Plus Counter = " + PlusCounter);
Console.WriteLine("Minus Counter = " + MinusCounter);
Console.WriteLine("Positive Ratio = " + PositiveRatio);
Console.WriteLine("Negative Ratio = " + NegativeRatio);
}
