public void SetSequenceAndMods(string sequence, IList <Modification> fixedMods, string variableMods)
{
Peptide = new CSMSL.Proteomics.Peptide(sequence);
Peptide.SetModifications(fixedMods);
Modificationstring = variableMods;
foreach (Tuple <Modification, int> modTuple in OmssaModification.ParseModificationLine(variableMods))
{
Modification mod = modTuple.Item1;
int site = modTuple.Item2;
if (site == 1 && mod.Sites.HasFlag(ModificationSites.NPep))
{
Peptide.AddModification(mod, Terminus.N);
}
else if (site == Peptide.Length && mod.Sites.HasFlag(ModificationSites.PepC))
{
Peptide.AddModification(mod, Terminus.C);
}
else
{
Peptide.AddModification(mod, site);
}
}
}
private List <PSM> LoadAllPSMs(string csvFile, string rawFileDirectory, List <Modification> fixedMods)
{
ProgressUpdate(0.0); //force the progressbar to go into marquee mode
Log("Reading PSMs from " + csvFile);
Dictionary <string, ThermoRawFile> rawFiles =
Directory.EnumerateFiles(rawFileDirectory, "*.raw", SearchOption.AllDirectories)
.ToDictionary(Path.GetFileNameWithoutExtension, file => new ThermoRawFile(file));
_dataFiles = new HashSet <MSDataFile>();
List <PSM> psms = new List <PSM>();
int totalPsms = 0;
using (CsvReader reader = new CsvReader(new StreamReader(csvFile), true))
{
while (reader.ReadNextRecord())
{
string mods = reader["Mods"];
totalPsms++;
// Skip if there are no modifications
if (string.IsNullOrEmpty(mods))
{
continue;
}
// Convert the text mod line into a list of modification objects
List <Modification> variableMods = OmssaModification.ParseModificationLine(mods).Select(item => item.Item1).ToList();
// Only keep things with quantified Modifications
if (!variableMods.Any(mod => QuantifiedModifications.Contains(mod)))
{
continue;
}
string filename = reader["Filename/id"];
string rawname = filename.Split('.')[0];
int scanNumber = int.Parse(reader["Spectrum number"]);
PSM psm = new PSM(scanNumber, rawname);
psm.StartResidue = int.Parse(reader["Start"]);
psm.Charge = int.Parse(reader["Charge"]);
psm.BasePeptide = new Peptide(reader["Peptide"].ToUpper());
psm.Defline = reader["Defline"];
psm.ProteinGroup = reader["Best PG Name"];
psm.NumberOfSharingProteinGroups = int.Parse(reader["# of Sharing PGs"]);
psm.Filename = filename;
// Apply all the fix modifications
psm.BasePeptide.SetModifications(fixedMods);
int i = 0;
while (i < variableMods.Count)
{
if (fixedMods.Contains(variableMods[i]))
{
variableMods.RemoveAt(i);
}
else
{
i++;
}
}
// Save all the variable mod types
psm.VariabledModifications = variableMods;
psms.Add(psm);
}
}
Log(string.Format("{0:N0} PSMs were loaded....", totalPsms));
Log(string.Format("{0:N0} PSMs were kept.... ({1:F2} %)", psms.Count, 100.0 * (double)psms.Count / totalPsms));
Log("Reading Spectral Data...");
ThermoRawFile currentRawFile = null;
string currentRawFileName = null;
int counter = 0;
foreach (PSM psm in psms.OrderBy(psm => psm.RawFileName))
{
string rawfilename = psm.RawFileName;
if (!rawfilename.Equals(currentRawFileName))
{
currentRawFileName = rawfilename;
if (currentRawFile != null && currentRawFile.IsOpen)
{
currentRawFile.Dispose();
}
if (!rawFiles.TryGetValue(rawfilename, out currentRawFile))
{
throw new NullReferenceException(string.Format("Raw File: {0}.raw was not found! Aborting.", rawfilename));
}
currentRawFile.Open();
}
psm.SetRawFile(currentRawFile);
counter++;
if (counter % 25 == 0)
{
ProgressUpdate((double)counter / psms.Count);
}
}
return(psms);
}
private List <Protein> CompileResults(List <LocalizedHit> hits, string csvFile, string outputDirectory, bool breakProteinsApart = false)
{
Dictionary <string, LocalizedHit> hitsdict = new Dictionary <string, LocalizedHit>();
// Group all the localized Hits into proteins
Dictionary <string, Protein> proteins = new Dictionary <string, Protein>();
foreach (LocalizedHit hit in hits)
{
hitsdict.Add(hit.PSM.Filename, hit);
string defline = hit.PSM.Defline;
if (breakProteinsApart)
{
string[] groups = hit.PSM.ProteinGroup.Split('|');
foreach (string group in groups)
{
Protein prot;
if (!proteins.TryGetValue(group, out prot))
{
prot = new Protein(group, defline);
proteins.Add(group, prot);
}
prot.AddHit(hit);
}
}
else
{
Protein prot;
if (!proteins.TryGetValue(hit.PSM.ProteinGroup, out prot))
{
prot = new Protein(hit.PSM.ProteinGroup, defline);
proteins.Add(hit.PSM.ProteinGroup, prot);
}
prot.AddHit(hit);
}
}
using (StreamWriter writer = new StreamWriter(Path.Combine(outputDirectory, Path.GetFileNameWithoutExtension(csvFile) + "_all.csv")),
localizedWriter = new StreamWriter(Path.Combine(outputDirectory, Path.GetFileNameWithoutExtension(csvFile) + "_localized.csv")))
{
using (CsvReader reader = new CsvReader(new StreamReader(csvFile), true))
{
LocalizedHit hit = null;
headerInfo = reader.GetFieldHeaders();
bool tqFound = false;
for (int i = 0; i < reader.FieldCount; i++)
{
if (headerInfo[i].EndsWith("NL)"))
{
if (!tqFound)
{
FirstQuantColumn = i;
tqFound = true;
}
}
if (headerInfo[i] == "Channels Detected")
{
LastQuantColumn = i - 1;
}
}
string header = string.Join(",", headerInfo) + ",# Isoforms,# of Considered Fragments,Localized?,Delta Score,Best Isoform,Spectral Matches,% TIC,Second Best Isoform,Second Spectral Matches,Second % TIC";
writer.WriteLine(header);
localizedWriter.WriteLine(header);
while (reader.ReadNextRecord())
{
string mods = reader["Mods"];
if (string.IsNullOrEmpty(mods))
{
continue;
}
List <Modification> variableMods = OmssaModification.ParseModificationLine(mods).Select(item => item.Item1).OfType <Modification>().ToList();
// Only keep things with quantified Modifications
if (!variableMods.Any(mod => QuantifiedModifications.Contains(mod)))
{
continue;
}
string filename = reader["Filename/id"];
if (!hitsdict.TryGetValue(filename, out hit))
{
continue;
}
string[] data = new string[reader.FieldCount];
reader.CopyCurrentRecordTo(data);
hit.omssapsm = data;
StringBuilder sb = new StringBuilder();
foreach (string datum in data)
{
if (datum.Contains(','))
{
sb.Append("\"");
sb.Append(datum);
sb.Append("\"");
}
else
{
sb.Append(datum);
}
sb.Append(',');
}
sb.Append(hit.PSM.Isoforms);
sb.Append(',');
sb.Append(hit.LocalizedIsoform.Fragments.Count);
sb.Append(',');
sb.Append(hit.IsLocalized);
sb.Append(',');
sb.Append(hit.MatchDifference);
sb.Append(',');
sb.Append(hit.LocalizedIsoform.SequenceWithModifications);
sb.Append(',');
sb.Append(hit.LocalizedIsoform.SpectralMatch.Matches);
sb.Append(',');
sb.Append(hit.LocalizedIsoform.SpectralMatch.PercentTIC);
if (hit.PSM.Isoforms > 1)
{
//sb.Append(',');
//sb.Append(hit.BestPeptideSDFCount);
sb.Append(',');
sb.Append(hit.SecondBestPeptideIsoform.SequenceWithModifications);
sb.Append(',');
sb.Append(hit.SecondBestPeptideIsoform.SpectralMatch.Matches);
sb.Append(',');
sb.Append(hit.SecondBestPeptideIsoform.SpectralMatch.PercentTIC);
//sb.Append(',');
//sb.Append(hit.SecondBestPeptideSDFCount);
}
if (hit.IsLocalized)
{
localizedWriter.WriteLine(sb.ToString());
}
writer.WriteLine(sb.ToString());
}
}
}
return(proteins.Values.ToList());
}