public void CalculateSequenceCoverage()
{
var proteinsWithUnambigSeqPsms = new Dictionary <Protein, List <PeptideWithSetModifications> >();
var proteinsWithPsmsWithLocalizedMods = new Dictionary <Protein, List <PeptideWithSetModifications> >();
foreach (var protein in Proteins)
{
proteinsWithUnambigSeqPsms.Add(protein, new List <PeptideWithSetModifications>());
proteinsWithPsmsWithLocalizedMods.Add(protein, new List <PeptideWithSetModifications>());
}
foreach (var psm in AllPsmsBelowOnePercentFDR)
{
// null BaseSequence means that the amino acid sequence is ambiguous; do not use these to calculate sequence coverage
if (psm.BaseSequence != null)
{
var PepsWithSetMods = psm.CompactPeptides.SelectMany(b => b.Value.Item2);
foreach (var pepWithSetMods in PepsWithSetMods)
{
// might be unambiguous but also shared; make sure this protein group contains this peptide+protein combo
if (Proteins.Contains(pepWithSetMods.Protein))
{
proteinsWithUnambigSeqPsms[pepWithSetMods.Protein].Add(pepWithSetMods);
// null FullSequence means that mods were not successfully localized; do not display them on the sequence coverage mods info
if (psm.FullSequence != null)
{
proteinsWithPsmsWithLocalizedMods[pepWithSetMods.Protein].Add(pepWithSetMods);
}
}
}
}
}
foreach (var protein in ListOfProteinsOrderedByAccession)
{
bool errorResult = false;
var sequenceCoverageDisplay = protein.BaseSequence.ToLower(CultureInfo.InvariantCulture);
HashSet <int> coveredOneBasedResidues = new HashSet <int>();
// get residue numbers of each peptide in the protein and identify them as observed if the sequence is unambiguous
foreach (var peptide in proteinsWithUnambigSeqPsms[protein])
{
string sequenceExtractedFromProtein = "";
for (int i = peptide.OneBasedStartResidueInProtein; i <= peptide.OneBasedEndResidueInProtein; i++)
{
// check for bugs in sequence coverage; make sure we have the right amino acids!
sequenceExtractedFromProtein += sequenceCoverageDisplay[i - 1];
coveredOneBasedResidues.Add(i);
}
if (!sequenceExtractedFromProtein.ToUpper().Equals(peptide.BaseSequence))
{
errorResult = true;
}
}
// calculate sequence coverage percent
double seqCoveragePercent = (double)coveredOneBasedResidues.Count / protein.Length;
if (seqCoveragePercent > 1)
{
errorResult = true;
}
// add the percent coverage or NaN if there was an error
if (!errorResult)
{
SequenceCoveragePercent.Add(seqCoveragePercent);
}
else
{
SequenceCoveragePercent.Add(double.NaN);
}
// convert the observed amino acids to upper case if they are unambiguously observed
var coverageArray = sequenceCoverageDisplay.ToCharArray();
foreach (var obsResidueLocation in coveredOneBasedResidues)
{
coverageArray[obsResidueLocation - 1] = char.ToUpper(coverageArray[obsResidueLocation - 1]);
}
sequenceCoverageDisplay = new string(coverageArray);
// check to see if there was an errored result; if not, add the coverage display
if (!errorResult)
{
SequenceCoverageDisplayList.Add(sequenceCoverageDisplay);
}
else
{
SequenceCoverageDisplayList.Add("Error calculating sequence coverage");
}
// put mods in the sequence coverage display
if (!errorResult)
{
// get mods to display in sequence (only unambiguously identified mods)
var modsOnThisProtein = new HashSet <KeyValuePair <int, ModificationWithMass> >();
foreach (var pep in proteinsWithPsmsWithLocalizedMods[protein])
{
foreach (var mod in pep.AllModsOneIsNterminus)
{
if (!mod.Value.modificationType.Contains("PeptideTermMod") && !mod.Value.modificationType.Contains("Common Variable") && !mod.Value.modificationType.Contains("Common Fixed"))
{
modsOnThisProtein.Add(new KeyValuePair <int, ModificationWithMass>(pep.OneBasedStartResidueInProtein + mod.Key - 2, mod.Value));
}
}
}
var temp1 = modsOnThisProtein.OrderBy(p => p.Key).ToList();
foreach (var mod in temp1)
{
if (mod.Value.terminusLocalization.Equals(TerminusLocalization.NProt))
{
sequenceCoverageDisplay = sequenceCoverageDisplay.Insert(0, "[" + mod.Value.id + "]-");
}
else if (mod.Value.terminusLocalization.Equals(TerminusLocalization.Any))
{
int modStringIndex = sequenceCoverageDisplay.Length - (protein.Length - mod.Key);
sequenceCoverageDisplay = sequenceCoverageDisplay.Insert(modStringIndex, "[" + mod.Value.id + "]");
}
else if (mod.Value.terminusLocalization.Equals(TerminusLocalization.ProtC))
{
sequenceCoverageDisplay = sequenceCoverageDisplay.Insert(sequenceCoverageDisplay.Length, "-[" + mod.Value.id + "]");
}
}
SequenceCoverageDisplayListWithMods.Add(sequenceCoverageDisplay);
if (modsOnThisProtein.Any())
{
// calculate spectral count percentage of modified observation
string tempModStrings = ""; //The whole string
List <int> tempPepModTotals = new List <int>(); //The List of (For one mod, The Modified Pep Num)
List <int> tempPepTotals = new List <int>(); //The List of (For one mod, The total Pep Num)
List <string> tempPepModValues = new List <string>(); //The List of (For one mod, the Modified Name)
List <int> tempModIndex = new List <int>(); //The Index of the modified position.
foreach (var pep in proteinsWithPsmsWithLocalizedMods[protein])
{
foreach (var mod in pep.AllModsOneIsNterminus)
{
int tempPepNumTotal = 0; //For one mod, The total Pep Num
if (!mod.Value.modificationType.Contains("Common Variable") && !mod.Value.modificationType.Contains("Common Fixed") && !mod.Value.terminusLocalization.Equals(TerminusLocalization.PepC) && !mod.Value.terminusLocalization.Equals(TerminusLocalization.NPep))
{
int tempIndexInProtein;
if (mod.Value.terminusLocalization.Equals(TerminusLocalization.NProt))
{
tempIndexInProtein = 1;
}
else if (mod.Value.terminusLocalization.Equals(TerminusLocalization.Any))
{
tempIndexInProtein = pep.OneBasedStartResidueInProtein + mod.Key - 2;
}
else if (mod.Value.terminusLocalization.Equals(TerminusLocalization.ProtC))
{
tempIndexInProtein = protein.Length;
}
else
{
// In case it's a peptide mod, skip!
continue;
}
if (tempModIndex.Contains(tempIndexInProtein) && tempPepModValues[tempModIndex.IndexOf(tempIndexInProtein)] == mod.Value.id)
{
tempPepModTotals[tempModIndex.IndexOf(tempIndexInProtein)] += 1;
}
else
{
tempModIndex.Add(tempIndexInProtein);
foreach (var pept in proteinsWithPsmsWithLocalizedMods[protein])
{
if (tempIndexInProtein >= pept.OneBasedStartResidueInProtein - (tempIndexInProtein == 1 ? 1 : 0) && tempIndexInProtein <= pept.OneBasedEndResidueInProtein)
{
tempPepNumTotal += 1;
}
}
tempPepTotals.Add(tempPepNumTotal);
tempPepModValues.Add(mod.Value.id);
tempPepModTotals.Add(1);
}
}
}
}
for (int i = 0; i < tempPepModTotals.Count; i++)
{
string tempString = ("#aa" + tempModIndex[i].ToString() + "[" + tempPepModValues[i].ToString() + ",info:occupancy=" + ((double)tempPepModTotals[i] / (double)tempPepTotals[i]).ToString("F2") + "(" + tempPepModTotals[i].ToString() + "/" + tempPepTotals[i].ToString() + ")" + "];");
tempModStrings += tempString;
}
if (!string.IsNullOrEmpty(tempModStrings))
{
ModsInfo.Add(tempModStrings);
}
}
}
}
}
public override string ToString()
{
var sb = new StringBuilder();
// list of protein accession numbers
sb.Append(ProteinGroupName);
sb.Append("\t");
// genes
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", ListOfProteinsOrderedByAccession.Select(p => p.GeneNames.Select(x => x.Item2).FirstOrDefault()))));
sb.Append("\t");
// organisms
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", ListOfProteinsOrderedByAccession.Select(p => p.Organism).Distinct())));
sb.Append("\t");
// list of protein names
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", ListOfProteinsOrderedByAccession.Select(p => p.FullName).Distinct())));
sb.Append("\t");
// list of masses
var sequences = ListOfProteinsOrderedByAccession.Select(p => p.BaseSequence).Distinct();
List <double> masses = new List <double>();
foreach (var sequence in sequences)
{
try
{
masses.Add(new Proteomics.AminoAcidPolymer.Peptide(sequence).MonoisotopicMass);
}
catch (System.Exception)
{
masses.Add(double.NaN);
}
}
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", masses)));
sb.Append("\t");
// number of proteins in group
sb.Append("" + Proteins.Count);
sb.Append("\t");
// list of unique peptides
if (!DisplayModsOnPeptides)
{
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", UniquePeptides.Select(p => p.BaseSequence).Distinct())));
}
else
{
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", UniquePeptides.Select(p => p.Sequence).Distinct())));
}
sb.Append("\t");
// list of shared peptides
var SharedPeptides = AllPeptides.Except(UniquePeptides);
if (!DisplayModsOnPeptides)
{
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", SharedPeptides.Select(p => p.BaseSequence).Distinct())));
}
else
{
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", SharedPeptides.Select(p => p.Sequence).Distinct())));
}
sb.Append("\t");
// number of peptides
if (!DisplayModsOnPeptides)
{
sb.Append("" + AllPeptides.Select(p => p.BaseSequence).Distinct().Count());
}
else
{
sb.Append("" + AllPeptides.Select(p => p.Sequence).Distinct().Count());
}
sb.Append("\t");
// number of unique peptides
if (!DisplayModsOnPeptides)
{
sb.Append("" + UniquePeptides.Select(p => p.BaseSequence).Distinct().Count());
}
else
{
sb.Append("" + UniquePeptides.Select(p => p.Sequence).Distinct().Count());
}
sb.Append("\t");
// sequence coverage percent
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", SequenceCoveragePercent.Select(p => string.Format("{0:0}" + "%", (p * 100))))));
sb.Append("\t");
// sequence coverage
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", SequenceCoverageDisplayList)));
sb.Append("\t");
// sequence coverage with mods
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", SequenceCoverageDisplayListWithMods)));
sb.Append("\t");
//Detailed mods information list
sb.Append(GlobalVariables.CheckLengthOfOutput(string.Join("|", ModsInfo)));
sb.Append("\t");
// MS1 intensity (retrieved from FlashLFQ in the SearchTask)
if (IntensitiesByFile != null && FilesForQuantification != null)
{
foreach (var file in FilesForQuantification)
{
if (IntensitiesByFile[file] > 0)
{
sb.Append(IntensitiesByFile[file]);
}
else
{
sb.Append("");
}
sb.Append("\t");
}
}
// number of PSMs for listed peptides
sb.Append("" + AllPsmsBelowOnePercentFDR.Count);
sb.Append("\t");
// isDecoy
if (IsDecoy)
{
sb.Append("D");
}
else if (IsContaminant)
{
sb.Append("C");
}
else
{
sb.Append("T");
}
sb.Append("\t");
// cumulative target
sb.Append(CumulativeTarget);
sb.Append("\t");
// cumulative decoy
sb.Append(CumulativeDecoy);
sb.Append("\t");
// q value
sb.Append(QValue);
sb.Append("\t");
// best peptide score
sb.Append(BestPeptideScore);
sb.Append("\t");
// best peptide q value
sb.Append(BestPeptideQValue);
sb.Append("\t");
return(sb.ToString());
}
