private static PsmFileType GetFileTypeFromHeader(string header)
{
PsmFileType type = PsmFileType.Unknown;
var split = header.Split('\t');
// MetaMorpheus MS/MS input
if (split.Contains("File Name") &&
split.Contains("Base Sequence") &&
split.Contains("Full Sequence") &&
split.Contains("Peptide Monoisotopic Mass") &&
split.Contains("Scan Retention Time") &&
split.Contains("Precursor Charge") &&
split.Contains("Protein Accession") &&
split.Contains("Decoy/Contaminant/Target") &&
split.Contains("QValue") &&
split.Contains("QValue Notch"))
{
_fileNameCol = Array.IndexOf(split, "File Name");
_baseSequCol = Array.IndexOf(split, "Base Sequence");
_fullSequCol = Array.IndexOf(split, "Full Sequence");
_monoMassCol = Array.IndexOf(split, "Peptide Monoisotopic Mass");
_msmsRetnCol = Array.IndexOf(split, "Scan Retention Time");
_chargeStCol = Array.IndexOf(split, "Precursor Charge");
_protNameCol = Array.IndexOf(split, "Protein Accession");
_decoyCol = Array.IndexOf(split, "Decoy/Contaminant/Target");
_qValueCol = Array.IndexOf(split, "QValue");
_qValueNotchCol = Array.IndexOf(split, "QValue Notch");
return(PsmFileType.MetaMorpheus);
}
// Morpheus MS/MS input
else if (split.Contains("Filename") &&
split.Contains("Base Peptide Sequence") &&
split.Contains("Peptide Sequence") &&
split.Contains("Theoretical Mass (Da)") &&
split.Contains("Retention Time (minutes)") &&
split.Contains("Precursor Charge") &&
split.Contains("Protein Description") &&
split.Contains("Decoy?") &&
split.Contains("Q-Value (%)"))
{
_fileNameCol = Array.IndexOf(split, "Filename");
_baseSequCol = Array.IndexOf(split, "Base Peptide Sequence");
_fullSequCol = Array.IndexOf(split, "Peptide Sequence");
_monoMassCol = Array.IndexOf(split, "Theoretical Mass (Da)");
_msmsRetnCol = Array.IndexOf(split, "Retention Time (minutes)");
_chargeStCol = Array.IndexOf(split, "Precursor Charge");
_protNameCol = Array.IndexOf(split, "Protein Description");
_decoyCol = Array.IndexOf(split, "Decoy?");
_qValueCol = Array.IndexOf(split, "Q-Value (%)");
return(PsmFileType.Morpheus);
}
// MaxQuant MS/MS input
else if (split.Contains("Raw file") &&
split.Contains("Sequence") &&
split.Contains("Modified sequence") &&
split.Contains("Mass") &&
split.Contains("Retention time") &&
split.Contains("Charge") &&
split.Contains("Proteins"))
{
_fileNameCol = Array.IndexOf(split, "Raw file");
_baseSequCol = Array.IndexOf(split, "Sequence");
_fullSequCol = Array.IndexOf(split, "Modified sequence");
_monoMassCol = Array.IndexOf(split, "Mass");
_msmsRetnCol = Array.IndexOf(split, "Retention time");
_chargeStCol = Array.IndexOf(split, "Charge");
_protNameCol = Array.IndexOf(split, "Proteins");
return(PsmFileType.MaxQuant);
}
// Peptide Shaker Input
else if (split.Contains("Spectrum File") &&
split.Contains("Sequence") &&
split.Contains("Modified Sequence") &&
split.Contains("Theoretical Mass") &&
split.Contains("RT") &&
split.Contains("Identification Charge") &&
split.Contains("Protein(s)"))
{
_fileNameCol = Array.IndexOf(split, "Spectrum File");
_baseSequCol = Array.IndexOf(split, "Sequence");
_fullSequCol = Array.IndexOf(split, "Modified Sequence");
_monoMassCol = Array.IndexOf(split, "Theoretical Mass");
_msmsRetnCol = Array.IndexOf(split, "RT");
_chargeStCol = Array.IndexOf(split, "Identification Charge");
_protNameCol = Array.IndexOf(split, "Protein(s)");
return(PsmFileType.PeptideShaker);
}
// TDPortal Input
else if (split.Contains("File Name") &&
split.Contains("Sequence") &&
split.Contains("Modifications") &&
split.Contains("Monoisotopic Mass") &&
split.Contains("RetentionTime") &&
split.Contains("Accession") &&
split.Contains("% Cleavages"))
{
_fileNameCol = Array.IndexOf(split, "File Name");
_baseSequCol = Array.IndexOf(split, "Sequence");
_fullSequCol = Array.IndexOf(split, "Modifications");
_monoMassCol = Array.IndexOf(split, "Monoisotopic Mass");
_msmsRetnCol = Array.IndexOf(split, "RetentionTime");
_protNameCol = Array.IndexOf(split, "Accession");
return(PsmFileType.TdPortal);
}
// Generic MS/MS input
if (split.Contains("File Name") &&
split.Contains("Base Sequence") &&
split.Contains("Full Sequence") &&
split.Contains("Peptide Monoisotopic Mass") &&
split.Contains("Scan Retention Time") &&
split.Contains("Precursor Charge") &&
split.Contains("Protein Accession"))
{
_fileNameCol = Array.IndexOf(split, "File Name");
_baseSequCol = Array.IndexOf(split, "Base Sequence");
_fullSequCol = Array.IndexOf(split, "Full Sequence");
_monoMassCol = Array.IndexOf(split, "Peptide Monoisotopic Mass");
_msmsRetnCol = Array.IndexOf(split, "Scan Retention Time");
_chargeStCol = Array.IndexOf(split, "Precursor Charge");
_protNameCol = Array.IndexOf(split, "Protein Accession");
return(PsmFileType.Generic);
}
return(type);
}
public static List <Identification> ReadPsms(string filepath, bool silent, List <SpectraFileInfo> rawfiles)
{
Dictionary <string, ProteinGroup> allProteinGroups = new Dictionary <string, ProteinGroup>();
_modSequenceToMonoMass = new Dictionary <string, double>();
List <Identification> ids = new List <Identification>();
PsmFileType fileType = PsmFileType.Unknown;
string[] delim = new string[] { ";", ",", " or ", "\"", "|" };
if (!silent)
{
Console.WriteLine("Opening PSM file " + filepath);
}
StreamReader reader;
try
{
reader = new StreamReader(filepath);
}
catch (Exception e)
{
if (!silent)
{
Console.WriteLine("Error reading file " + filepath + "\n" + e.Message);
}
return(new List <Identification>());
}
int lineNum = 1;
while (reader.Peek() > 0)
{
string line = reader.ReadLine();
try
{
if (lineNum != 1)
{
if (fileType == PsmFileType.Unknown)
{
break;
}
var param = line.Split('\t');
// only quantify PSMs below 1% FDR
if (fileType == PsmFileType.MetaMorpheus && double.Parse(param[_qValueCol]) > 0.01)
{
break;
}
else if (fileType == PsmFileType.Morpheus && double.Parse(param[_qValueCol]) > 1.00)
{
break;
}
// only quantify PSMs below 1% notch FDR
if (fileType == PsmFileType.MetaMorpheus && double.Parse(param[_qValueNotchCol]) > 0.01)
{
continue;
}
// skip decoys
if ((fileType == PsmFileType.MetaMorpheus || fileType == PsmFileType.Morpheus) &&
param[_decoyCol].Contains("D"))
{
continue;
}
// spectrum file name
string fileName = param[_fileNameCol];
// base sequence
string baseSequence = param[_baseSequCol];
// skip ambiguous sequence in MetaMorpheus output
if (fileType == PsmFileType.MetaMorpheus && (baseSequence.Contains(" or ") || baseSequence.Contains("|")))
{
lineNum++;
continue;
}
// modified sequence
string modSequence = param[_fullSequCol];
if (fileType == PsmFileType.TdPortal)
{
modSequence = baseSequence + modSequence;
}
// skip ambiguous sequence in MetaMorpheus output
if (fileType == PsmFileType.MetaMorpheus && (modSequence.Contains(" or ") || modSequence.Contains("|") || modSequence.Contains("too long")))
{
lineNum++;
continue;
}
// monoisotopic mass
double monoisotopicMass = double.Parse(param[_monoMassCol]);
if (_modSequenceToMonoMass.TryGetValue(modSequence, out double storedMonoisotopicMass))
{
if (storedMonoisotopicMass != monoisotopicMass)
{
if (!silent)
{
Console.WriteLine("Caution! PSM with sequence " + modSequence + " at line " +
lineNum + " could not be read; " +
"a peptide with the same modified sequence but a different monoisotopic mass has already been added");
}
lineNum++;
continue;
}
}
else
{
_modSequenceToMonoMass.Add(modSequence, monoisotopicMass);
}
// retention time
double ms2RetentionTime = double.Parse(param[_msmsRetnCol]);
if (fileType == PsmFileType.PeptideShaker)
{
// peptide shaker RT is in seconds - convert to minutes
ms2RetentionTime = ms2RetentionTime / 60.0;
}
if (ms2RetentionTime < 0)
{
if (!silent)
{
Console.WriteLine("Caution! PSM with sequence " + modSequence + " at line " +
lineNum + " could not be read; retention time was negative");
}
lineNum++;
continue;
}
// charge state
int chargeState;
if (fileType == PsmFileType.TdPortal)
{
chargeState = 1;
}
else if (fileType == PsmFileType.PeptideShaker)
{
string charge = new String(param[_chargeStCol].Where(Char.IsDigit).ToArray());
chargeState = int.Parse(charge);
}
else
{
chargeState = (int)double.Parse(param[_chargeStCol]);
}
// protein groups
List <string> proteinGroupStrings = new List <string>();
if (fileType == PsmFileType.MetaMorpheus)
{
// MetaMorpheus - use all proteins listed
var g = param[_protNameCol].Split(delim, StringSplitOptions.RemoveEmptyEntries);
if (g.Any())
{
foreach (var pg in g)
{
proteinGroupStrings.Add(pg.Trim());
}
}
}
else if (fileType == PsmFileType.Morpheus)
{
// Morpheus - only one protein listed, use it
proteinGroupStrings.Add(param[_protNameCol].Trim());
}
else if (fileType == PsmFileType.MaxQuant)
{
// MaxQuant - use the first protein listed
var g = param[_protNameCol].Split(delim, StringSplitOptions.RemoveEmptyEntries);
if (g.Any())
{
proteinGroupStrings.Add(g.First().Trim());
}
}
else if (fileType == PsmFileType.PeptideShaker)
{
// Peptide Shaker - use all proteins listed
var g = param[_protNameCol].Split(delim, StringSplitOptions.RemoveEmptyEntries);
if (g.Any())
{
foreach (var pg in g)
{
proteinGroupStrings.Add(pg.Trim());
}
}
}
else if (fileType == PsmFileType.TdPortal)
{
// TDPortal - use base sequence as protein group
proteinGroupStrings.Add(baseSequence);
}
else
{
proteinGroupStrings.Add(param[_protNameCol]);
}
List <ProteinGroup> proteinGroups = new List <ProteinGroup>();
foreach (var proteinGroupName in proteinGroupStrings)
{
if (allProteinGroups.TryGetValue(proteinGroupName, out ProteinGroup pg))
{
proteinGroups.Add(pg);
}
else
{
ProteinGroup newPg = new ProteinGroup(proteinGroupName, "", "");
allProteinGroups.Add(proteinGroupName, newPg);
proteinGroups.Add(newPg);
}
}
// construct id
var fileNameNoExt = Path.GetFileNameWithoutExtension(fileName);
var rawFileInfoToUse = rawfiles.FirstOrDefault(p => p.FilenameWithoutExtension.Equals(fileNameNoExt));
if (rawFileInfoToUse == null)
{
// skip PSMs for files with no spectrum data input
lineNum++;
continue;
}
var ident = new Identification(rawFileInfoToUse, baseSequence, modSequence, monoisotopicMass, ms2RetentionTime, chargeState, proteinGroups);
ids.Add(ident);
}
else
{
fileType = GetFileTypeFromHeader(line);
}
lineNum++;
}
catch (Exception)
{
if (!silent)
{
Console.WriteLine("Problem reading line " + lineNum + " of the identification file");
}
return(new List <Identification>());
}
}
if (fileType == PsmFileType.Unknown)
{
throw new Exception("Could not interpret PSM header labels from file: " + filepath);
}
reader.Close();
if (!silent)
{
Console.WriteLine("Done reading PSMs; found " + ids.Count);
}
return(ids);
}
private static PsmFileType GetFileTypeFromHeader(string header)
{
PsmFileType type = PsmFileType.Unknown;
var split = header.Split('\t').Select(p => p.ToLowerInvariant()).ToArray();
// MetaMorpheus MS/MS input
if (split.Contains("File Name".ToLowerInvariant()) &&
split.Contains("Base Sequence".ToLowerInvariant()) &&
split.Contains("Full Sequence".ToLowerInvariant()) &&
split.Contains("Peptide Monoisotopic Mass".ToLowerInvariant()) &&
split.Contains("Scan Retention Time".ToLowerInvariant()) &&
split.Contains("Precursor Charge".ToLowerInvariant()) &&
split.Contains("Protein Accession".ToLowerInvariant()) &&
split.Contains("Decoy/Contaminant/Target".ToLowerInvariant()) &&
split.Contains("QValue".ToLowerInvariant()) &&
split.Contains("QValue Notch".ToLowerInvariant()))
{
_fileNameCol = Array.IndexOf(split, "File Name".ToLowerInvariant());
_baseSequCol = Array.IndexOf(split, "Base Sequence".ToLowerInvariant());
_fullSequCol = Array.IndexOf(split, "Full Sequence".ToLowerInvariant());
_monoMassCol = Array.IndexOf(split, "Peptide Monoisotopic Mass".ToLowerInvariant());
_msmsRetnCol = Array.IndexOf(split, "Scan Retention Time".ToLowerInvariant());
_chargeStCol = Array.IndexOf(split, "Precursor Charge".ToLowerInvariant());
_protNameCol = Array.IndexOf(split, "Protein Accession".ToLowerInvariant());
_decoyCol = Array.IndexOf(split, "Decoy/Contaminant/Target".ToLowerInvariant());
_qValueCol = Array.IndexOf(split, "QValue".ToLowerInvariant());
_qValueNotchCol = Array.IndexOf(split, "QValue Notch".ToLowerInvariant());
_geneNameCol = Array.IndexOf(split, "Gene Name".ToLowerInvariant());
_organismCol = Array.IndexOf(split, "Organism Name".ToLowerInvariant());
return(PsmFileType.MetaMorpheus);
}
// Morpheus MS/MS input
else if (split.Contains("Filename".ToLowerInvariant()) &&
split.Contains("Base Peptide Sequence".ToLowerInvariant()) &&
split.Contains("Peptide Sequence".ToLowerInvariant()) &&
split.Contains("Theoretical Mass (Da)".ToLowerInvariant()) &&
split.Contains("Retention Time (minutes)".ToLowerInvariant()) &&
split.Contains("Precursor Charge".ToLowerInvariant()) &&
split.Contains("Protein Description".ToLowerInvariant()) &&
split.Contains("Decoy?".ToLowerInvariant()) &&
split.Contains("Q-Value (%)".ToLowerInvariant()))
{
_fileNameCol = Array.IndexOf(split, "Filename".ToLowerInvariant());
_baseSequCol = Array.IndexOf(split, "Base Peptide Sequence".ToLowerInvariant());
_fullSequCol = Array.IndexOf(split, "Peptide Sequence".ToLowerInvariant());
_monoMassCol = Array.IndexOf(split, "Theoretical Mass (Da)".ToLowerInvariant());
_msmsRetnCol = Array.IndexOf(split, "Retention Time (minutes)".ToLowerInvariant());
_chargeStCol = Array.IndexOf(split, "Precursor Charge".ToLowerInvariant());
_protNameCol = Array.IndexOf(split, "Protein Description".ToLowerInvariant());
_decoyCol = Array.IndexOf(split, "Decoy?".ToLowerInvariant());
_qValueCol = Array.IndexOf(split, "Q-Value (%)".ToLowerInvariant());
_geneNameCol = Array.IndexOf(split, "Gene Name".ToLowerInvariant()); // probably doesn't exist
_organismCol = Array.IndexOf(split, "Organism Name".ToLowerInvariant());
return(PsmFileType.Morpheus);
}
// MaxQuant MS/MS input
else if (split.Contains("Raw file".ToLowerInvariant()) &&
split.Contains("Sequence".ToLowerInvariant()) &&
split.Contains("Modified sequence".ToLowerInvariant()) &&
split.Contains("Mass".ToLowerInvariant()) &&
split.Contains("Retention time".ToLowerInvariant()) &&
split.Contains("Charge".ToLowerInvariant()) &&
split.Contains("Proteins".ToLowerInvariant()))
{
_fileNameCol = Array.IndexOf(split, "Raw file".ToLowerInvariant());
_baseSequCol = Array.IndexOf(split, "Sequence".ToLowerInvariant());
_fullSequCol = Array.IndexOf(split, "Modified sequence".ToLowerInvariant());
_monoMassCol = Array.IndexOf(split, "Mass".ToLowerInvariant());
_msmsRetnCol = Array.IndexOf(split, "Retention time".ToLowerInvariant());
_chargeStCol = Array.IndexOf(split, "Charge".ToLowerInvariant());
_protNameCol = Array.IndexOf(split, "Proteins".ToLowerInvariant());
_geneNameCol = Array.IndexOf(split, "Gene Names".ToLowerInvariant());
_organismCol = Array.IndexOf(split, "Organism Name".ToLowerInvariant());
return(PsmFileType.MaxQuant);
}
// Peptide Shaker Input
else if (split.Contains("Spectrum File".ToLowerInvariant()) &&
split.Contains("Sequence".ToLowerInvariant()) &&
split.Contains("Modified Sequence".ToLowerInvariant()) &&
split.Contains("Theoretical Mass".ToLowerInvariant()) &&
split.Contains("RT".ToLowerInvariant()) &&
split.Contains("Identification Charge".ToLowerInvariant()) &&
split.Contains("Protein(s)".ToLowerInvariant()))
{
_fileNameCol = Array.IndexOf(split, "Spectrum File".ToLowerInvariant());
_baseSequCol = Array.IndexOf(split, "Sequence".ToLowerInvariant());
_fullSequCol = Array.IndexOf(split, "Modified Sequence".ToLowerInvariant());
_monoMassCol = Array.IndexOf(split, "Theoretical Mass".ToLowerInvariant());
_msmsRetnCol = Array.IndexOf(split, "RT".ToLowerInvariant());
_chargeStCol = Array.IndexOf(split, "Identification Charge".ToLowerInvariant());
_protNameCol = Array.IndexOf(split, "Protein(s)".ToLowerInvariant());
_geneNameCol = Array.IndexOf(split, "Gene Name".ToLowerInvariant()); // probably doesn't exist
_organismCol = Array.IndexOf(split, "Organism Name".ToLowerInvariant());
return(PsmFileType.PeptideShaker);
}
// Generic MS/MS input
if (split.Contains("File Name".ToLowerInvariant()) &&
split.Contains("Base Sequence".ToLowerInvariant()) &&
split.Contains("Full Sequence".ToLowerInvariant()) &&
split.Contains("Peptide Monoisotopic Mass".ToLowerInvariant()) &&
split.Contains("Scan Retention Time".ToLowerInvariant()) &&
split.Contains("Precursor Charge".ToLowerInvariant()) &&
split.Contains("Protein Accession".ToLowerInvariant()))
{
_fileNameCol = Array.IndexOf(split, "File Name".ToLowerInvariant());
_baseSequCol = Array.IndexOf(split, "Base Sequence".ToLowerInvariant());
_fullSequCol = Array.IndexOf(split, "Full Sequence".ToLowerInvariant());
_monoMassCol = Array.IndexOf(split, "Peptide Monoisotopic Mass".ToLowerInvariant());
_msmsRetnCol = Array.IndexOf(split, "Scan Retention Time".ToLowerInvariant());
_chargeStCol = Array.IndexOf(split, "Precursor Charge".ToLowerInvariant());
_protNameCol = Array.IndexOf(split, "Protein Accession".ToLowerInvariant());
_geneNameCol = Array.IndexOf(split, "Gene Name".ToLowerInvariant()); // probably doesn't exist
_organismCol = Array.IndexOf(split, "Organism Name".ToLowerInvariant());
return(PsmFileType.Generic);
}
return(type);
}
public static List <Identification> ReadPsms(string filepath, bool silent, List <SpectraFileInfo> rawfiles)
{
if (_modSequenceToMonoMass == null)
{
_modSequenceToMonoMass = new Dictionary <string, double>();
}
if (allProteinGroups == null)
{
allProteinGroups = new Dictionary <string, ProteinGroup>();
}
var rawFileDictionary = rawfiles.ToDictionary(p => p.FilenameWithoutExtension, v => v);
List <Identification> ids = new List <Identification>();
PsmFileType fileType = PsmFileType.Unknown;
if (!silent)
{
Console.WriteLine("Opening PSM file " + filepath);
}
StreamReader reader;
try
{
reader = new StreamReader(filepath);
}
catch (Exception e)
{
if (!silent)
{
Console.WriteLine("Error reading file " + filepath + "\n" + e.Message);
}
return(new List <Identification>());
}
int lineNum = 0;
while (reader.Peek() > 0)
{
string line = reader.ReadLine();
lineNum++;
try
{
if (lineNum == 1)
{
fileType = GetFileTypeFromHeader(line);
if (fileType == PsmFileType.Unknown)
{
throw new Exception("Could not interpret PSM header labels from file: " + filepath);
}
}
else
{
var param = line.Split('\t');
// only quantify PSMs below 1% FDR
if (fileType == PsmFileType.MetaMorpheus && double.Parse(param[_qValueCol], CultureInfo.InvariantCulture) > 0.01)
{
break;
}
else if (fileType == PsmFileType.Morpheus && double.Parse(param[_qValueCol], CultureInfo.InvariantCulture) > 1.00)
{
break;
}
// only quantify PSMs below 1% notch FDR
if (fileType == PsmFileType.MetaMorpheus && double.Parse(param[_qValueNotchCol], CultureInfo.InvariantCulture) > 0.01)
{
continue;
}
// skip decoys
if ((fileType == PsmFileType.MetaMorpheus || fileType == PsmFileType.Morpheus) &&
param[_decoyCol].Contains("D"))
{
continue;
}
// spectrum file name
string fileName = param[_fileNameCol];
// base sequence
string baseSequence = param[_baseSequCol];
// modified sequence
string modSequence = param[_fullSequCol];
// skip ambiguous sequence in MetaMorpheus output
if (fileType == PsmFileType.MetaMorpheus && (modSequence.Contains(" or ") || modSequence.Contains("|") || modSequence.ToLowerInvariant().Contains("too long")))
{
continue;
}
// monoisotopic mass
if (double.TryParse(param[_monoMassCol], NumberStyles.Number, CultureInfo.InvariantCulture, out double monoisotopicMass))
{
if (_modSequenceToMonoMass.TryGetValue(modSequence, out double storedMonoisotopicMass))
{
if (storedMonoisotopicMass != monoisotopicMass)
{
if (!silent)
{
Console.WriteLine("Caution! PSM with sequence " + modSequence + " at line " +
lineNum + " could not be read; " +
"a peptide with the same modified sequence but a different monoisotopic mass has already been added");
}
continue;
}
}
else
{
_modSequenceToMonoMass.Add(modSequence, monoisotopicMass);
}
}
else
{
if (!silent)
{
Console.WriteLine("PSM with sequence " + modSequence + " at line " +
lineNum + " could not be read; " +
"monoisotopic mass was not interpretable: \"" + param[_monoMassCol] + "\"");
}
continue;
}
// retention time
if (double.TryParse(param[_msmsRetnCol], out double ms2RetentionTime))
{
if (fileType == PsmFileType.PeptideShaker)
{
// peptide shaker RT is in seconds - convert to minutes
ms2RetentionTime = ms2RetentionTime / 60.0;
}
if (ms2RetentionTime < 0)
{
if (!silent)
{
Console.WriteLine("Caution! PSM with sequence " + modSequence + " at line " +
lineNum + " could not be read; retention time was negative");
}
continue;
}
}
else
{
if (!silent)
{
Console.WriteLine("PSM with sequence " + modSequence + " at line " +
lineNum + " could not be read; " +
"retention time was not interpretable: \"" + param[_msmsRetnCol] + "\"");
}
continue;
}
// charge state
int chargeState;
if (fileType == PsmFileType.PeptideShaker)
{
string chargeStringNumbersOnly = new String(param[_chargeStCol].Where(Char.IsDigit).ToArray());
if (string.IsNullOrWhiteSpace(chargeStringNumbersOnly))
{
if (!silent)
{
Console.WriteLine("PSM with sequence " + modSequence + " at line " +
lineNum + " could not be read; " +
"charge state was not interpretable: \"" + param[_chargeStCol] + "\"");
}
continue;
}
else
{
if (!int.TryParse(chargeStringNumbersOnly, out chargeState))
{
if (!silent)
{
Console.WriteLine("PSM with sequence " + modSequence + " at line " +
lineNum + " could not be read; " +
"charge state was not interpretable: \"" + param[_chargeStCol] + "\"");
}
continue;
}
}
}
else
{
if (!double.TryParse(param[_chargeStCol], out double chargeStateDouble))
{
if (!silent)
{
Console.WriteLine("PSM with sequence " + modSequence + " at line " +
lineNum + " could not be read; " +
"charge state was not interpretable: \"" + param[_chargeStCol] + "\"");
}
continue;
}
chargeState = (int)chargeStateDouble;
}
// protein groups
// use all proteins listed
List <ProteinGroup> proteinGroups = new List <ProteinGroup>();
var proteins = param[_protNameCol].Split(delimiters[fileType], StringSplitOptions.None);
string[] genes = null;
if (_geneNameCol >= 0)
{
genes = param[_geneNameCol].Split(delimiters[fileType], StringSplitOptions.None);
}
string[] organisms = null;
if (_organismCol >= 0)
{
organisms = param[_organismCol].Split(delimiters[fileType], StringSplitOptions.None);
}
for (int pr = 0; pr < proteins.Length; pr++)
{
string proteinName = proteins[pr];
string gene = "";
string organism = "";
if (genes != null)
{
if (genes.Length == 1)
{
gene = genes[0];
}
else if (genes.Length == proteins.Length)
{
gene = genes[pr];
}
else if (proteins.Length == 1)
{
gene = param[_geneNameCol];
}
}
if (organisms != null)
{
if (organisms.Length == 1)
{
organism = organisms[0];
}
else if (organisms.Length == proteins.Length)
{
organism = organisms[pr];
}
else if (proteins.Length == 1)
{
organism = param[_organismCol];
}
}
if (allProteinGroups.TryGetValue(proteinName, out ProteinGroup pg))
{
proteinGroups.Add(pg);
}
else
{
ProteinGroup newPg = new ProteinGroup(proteinName, gene, organism);
allProteinGroups.Add(proteinName, newPg);
proteinGroups.Add(newPg);
}
}
// get file name and look up file name object
var fileNameNoExt = Path.GetFileNameWithoutExtension(fileName);
if (!rawFileDictionary.TryGetValue(fileNameNoExt, out SpectraFileInfo spectraFileInfoToUse))
{
// skip PSMs for files with no spectrum data input
continue;
}
// construct id
var ident = new Identification(spectraFileInfoToUse, baseSequence, modSequence, monoisotopicMass, ms2RetentionTime, chargeState, proteinGroups);
ids.Add(ident);
}
}
catch (Exception)
{
if (!silent)
{
Console.WriteLine("Problem reading line " + lineNum + " of the identification file");
}
return(new List <Identification>());
}
}
reader.Close();
if (!silent)
{
Console.WriteLine("Done reading PSMs; found " + ids.Count);
}
return(ids);
}
private static PsmFileType GetFileTypeFromHeader(string header)
{
PsmFileType type = PsmFileType.Unknown;
var split = header.Split('\t').Select(p => p.ToLowerInvariant()).ToArray();
// MetaMorpheus MS/MS input
if (split.Contains("File Name".ToLowerInvariant()) &&
split.Contains("Base Sequence".ToLowerInvariant()) &&
split.Contains("Full Sequence".ToLowerInvariant()) &&
split.Contains("Peptide Monoisotopic Mass".ToLowerInvariant()) &&
split.Contains("Scan Retention Time".ToLowerInvariant()) &&
split.Contains("Precursor Charge".ToLowerInvariant()) &&
split.Contains("Protein Accession".ToLowerInvariant()) &&
split.Contains("Decoy/Contaminant/Target".ToLowerInvariant()) &&
split.Contains("QValue".ToLowerInvariant()) &&
split.Contains("QValue Notch".ToLowerInvariant()))
{
_fileNameCol = Array.IndexOf(split, "File Name".ToLowerInvariant());
_baseSequCol = Array.IndexOf(split, "Base Sequence".ToLowerInvariant());
_fullSequCol = Array.IndexOf(split, "Full Sequence".ToLowerInvariant());
_monoMassCol = Array.IndexOf(split, "Peptide Monoisotopic Mass".ToLowerInvariant());
_msmsRetnCol = Array.IndexOf(split, "Scan Retention Time".ToLowerInvariant());
_chargeStCol = Array.IndexOf(split, "Precursor Charge".ToLowerInvariant());
_protNameCol = Array.IndexOf(split, "Protein Accession".ToLowerInvariant());
_decoyCol = Array.IndexOf(split, "Decoy/Contaminant/Target".ToLowerInvariant());
_qValueCol = Array.IndexOf(split, "QValue".ToLowerInvariant());
_qValueNotchCol = Array.IndexOf(split, "QValue Notch".ToLowerInvariant());
_geneNameCol = Array.IndexOf(split, "Gene Name".ToLowerInvariant());
_organismCol = Array.IndexOf(split, "Organism Name".ToLowerInvariant());
return(PsmFileType.MetaMorpheus);
}
// Morpheus MS/MS input
else if (split.Contains("Filename".ToLowerInvariant()) &&
split.Contains("Base Peptide Sequence".ToLowerInvariant()) &&
split.Contains("Peptide Sequence".ToLowerInvariant()) &&
split.Contains("Theoretical Mass (Da)".ToLowerInvariant()) &&
split.Contains("Retention Time (minutes)".ToLowerInvariant()) &&
split.Contains("Precursor Charge".ToLowerInvariant()) &&
split.Contains("Protein Description".ToLowerInvariant()) &&
split.Contains("Decoy?".ToLowerInvariant()) &&
split.Contains("Q-Value (%)".ToLowerInvariant()))
{
_fileNameCol = Array.IndexOf(split, "Filename".ToLowerInvariant());
_baseSequCol = Array.IndexOf(split, "Base Peptide Sequence".ToLowerInvariant());
_fullSequCol = Array.IndexOf(split, "Peptide Sequence".ToLowerInvariant());
_monoMassCol = Array.IndexOf(split, "Theoretical Mass (Da)".ToLowerInvariant());
_msmsRetnCol = Array.IndexOf(split, "Retention Time (minutes)".ToLowerInvariant());
_chargeStCol = Array.IndexOf(split, "Precursor Charge".ToLowerInvariant());
_protNameCol = Array.IndexOf(split, "Protein Description".ToLowerInvariant());
_decoyCol = Array.IndexOf(split, "Decoy?".ToLowerInvariant());
_qValueCol = Array.IndexOf(split, "Q-Value (%)".ToLowerInvariant());
_geneNameCol = Array.IndexOf(split, "Gene Name".ToLowerInvariant()); // probably doesn't exist
_organismCol = Array.IndexOf(split, "Organism Name".ToLowerInvariant());
return(PsmFileType.Morpheus);
}
// MaxQuant MS/MS input
else if (split.Contains("Raw file".ToLowerInvariant()) &&
split.Contains("Sequence".ToLowerInvariant()) &&
split.Contains("Modified sequence".ToLowerInvariant()) &&
split.Contains("Mass".ToLowerInvariant()) &&
split.Contains("Retention time".ToLowerInvariant()) &&
split.Contains("Charge".ToLowerInvariant()) &&
split.Contains("Proteins".ToLowerInvariant()))
{
_fileNameCol = Array.IndexOf(split, "Raw file".ToLowerInvariant());
_baseSequCol = Array.IndexOf(split, "Sequence".ToLowerInvariant());
_fullSequCol = Array.IndexOf(split, "Modified sequence".ToLowerInvariant());
_monoMassCol = Array.IndexOf(split, "Mass".ToLowerInvariant());
_msmsRetnCol = Array.IndexOf(split, "Retention time".ToLowerInvariant());
_chargeStCol = Array.IndexOf(split, "Charge".ToLowerInvariant());
_protNameCol = Array.IndexOf(split, "Proteins".ToLowerInvariant());
_geneNameCol = Array.IndexOf(split, "Gene Names".ToLowerInvariant());
_organismCol = Array.IndexOf(split, "Organism Name".ToLowerInvariant());
return(PsmFileType.MaxQuant);
}
// Peptide Shaker Input
else if (split.Contains("Spectrum File".ToLowerInvariant()) &&
split.Contains("Sequence".ToLowerInvariant()) &&
split.Contains("Modified Sequence".ToLowerInvariant()) &&
split.Contains("Theoretical Mass".ToLowerInvariant()) &&
split.Contains("RT".ToLowerInvariant()) &&
split.Contains("Identification Charge".ToLowerInvariant()) &&
split.Contains("Protein(s)".ToLowerInvariant()))
{
_fileNameCol = Array.IndexOf(split, "Spectrum File".ToLowerInvariant());
_baseSequCol = Array.IndexOf(split, "Sequence".ToLowerInvariant());
_fullSequCol = Array.IndexOf(split, "Modified Sequence".ToLowerInvariant());
_monoMassCol = Array.IndexOf(split, "Theoretical Mass".ToLowerInvariant());
_msmsRetnCol = Array.IndexOf(split, "RT".ToLowerInvariant());
_chargeStCol = Array.IndexOf(split, "Identification Charge".ToLowerInvariant());
_protNameCol = Array.IndexOf(split, "Protein(s)".ToLowerInvariant());
_geneNameCol = Array.IndexOf(split, "Gene Name".ToLowerInvariant()); // probably doesn't exist
_organismCol = Array.IndexOf(split, "Organism Name".ToLowerInvariant());
return(PsmFileType.PeptideShaker);
}
// Percolator Input
// Assume that no decoy are provided in this input
else if (split.Contains("file_idx".ToLowerInvariant()) &&
split.Contains("scan".ToLowerInvariant()) &&
split.Contains("charge".ToLowerInvariant()) &&
split.Contains("spectrum neutral mass".ToLowerInvariant()) && //experimental neutral mass
split.Contains("peptide mass".ToLowerInvariant()) && //theoretical neutral (uncharged) peptide mass
split.Contains("sequence".ToLowerInvariant()) &&
split.Contains("protein id".ToLowerInvariant()))
{
_fileNameCol = Array.IndexOf(split, "file_idx".ToLowerInvariant());
_fullSequCol = Array.IndexOf(split, "sequence".ToLowerInvariant());
_monoMassCol = Array.IndexOf(split, "peptide mass".ToLowerInvariant()); //TODO: see if this needs to be theoretical or experimental mass AND if it is neutral or monoisotopic(H+)
_msmsScanCol = Array.IndexOf(split, "scan".ToLowerInvariant());
_chargeStCol = Array.IndexOf(split, "charge".ToLowerInvariant());
_protNameCol = Array.IndexOf(split, "protein id".ToLowerInvariant());
_qValueCol = Array.IndexOf(split, "percolator q-value".ToLowerInvariant());
return(PsmFileType.Percolator);
}
// Generic MS/MS input
if (split.Contains("File Name".ToLowerInvariant()) &&
split.Contains("Base Sequence".ToLowerInvariant()) &&
split.Contains("Full Sequence".ToLowerInvariant()) &&
split.Contains("Peptide Monoisotopic Mass".ToLowerInvariant()) &&
split.Contains("Scan Retention Time".ToLowerInvariant()) &&
split.Contains("Precursor Charge".ToLowerInvariant()) &&
split.Contains("Protein Accession".ToLowerInvariant()))
{
_fileNameCol = Array.IndexOf(split, "File Name".ToLowerInvariant());
_baseSequCol = Array.IndexOf(split, "Base Sequence".ToLowerInvariant());
_fullSequCol = Array.IndexOf(split, "Full Sequence".ToLowerInvariant());
_monoMassCol = Array.IndexOf(split, "Peptide Monoisotopic Mass".ToLowerInvariant());
_msmsRetnCol = Array.IndexOf(split, "Scan Retention Time".ToLowerInvariant());
_chargeStCol = Array.IndexOf(split, "Precursor Charge".ToLowerInvariant());
_protNameCol = Array.IndexOf(split, "Protein Accession".ToLowerInvariant());
_geneNameCol = Array.IndexOf(split, "Gene Name".ToLowerInvariant()); // probably doesn't exist
_organismCol = Array.IndexOf(split, "Organism Name".ToLowerInvariant());
return(PsmFileType.Generic);
}
return(type);
}