public static Dictionary <string, Modification> ReadUniProtXmlModifications(string uniProtXmlProteomeDatabaseFilepath)
{
if (proteinExistenceCodes == null)
{
InitializeDictionaries();
}
List <string> modifications_in_database = new List <string>();
using (XmlReader xml = XmlReader.Create(uniProtXmlProteomeDatabaseFilepath))
{
while (xml.ReadToFollowing("feature"))
{
if (xml.GetAttribute("type") == "modified residue" && (!ONLY_CONSIDER_MODIFICATIONS_WITH_EVIDENCE || xml.GetAttribute("evidence") != null))
{
string description = xml.GetAttribute("description");
if (!description.Contains("variant"))
{
int semicolon_index = description.IndexOf(';');
if (semicolon_index >= 0)
{
description = description.Substring(0, semicolon_index);
}
modifications_in_database.Add(description);
}
}
}
}
Dictionary <string, Modification> modifications = new Dictionary <string, Modification>();
ModificationDictionary user_modifications = ModificationDictionary.Instance;
int i = 0;
while (i < modifications_in_database.Count)
{
string modification_name = modifications_in_database[i];
Modification modification;
if (user_modifications.TryGetValue(modification_name, out modification))
{
modifications.Add("UniProt: " + modification_name, new Modification("UniProt: " + modification_name, modification.Type, modification.AminoAcid, modification.MonoisotopicMassShift, modification.AverageMassShift, modification.MonoisotopicNeutralLossMass, modification.AverageNeutralLossMass, false, true, modification.Database, modification.DatabaseAccessionNumber, modification.DatabaseName, true));
modifications_in_database.RemoveAt(i);
}
else
{
i++;
}
}
if (modifications_in_database.Count > 0)
{
string old_ptmlist_filepath = Path.Combine(Path.GetDirectoryName(Environment.GetCommandLineArgs()[0]), "ptmlist.txt");
try
{
string new_ptmlist_filepath = Path.Combine(Path.GetDirectoryName(Environment.GetCommandLineArgs()[0]), "ptmlist.new.txt");
using (WebClient client = new WebClient())
{
client.DownloadFile("http://www.uniprot.org/docs/ptmlist.txt", new_ptmlist_filepath);
}
string old_ptmlist = File.ReadAllText(old_ptmlist_filepath);
string new_ptmlist = File.ReadAllText(new_ptmlist_filepath);
if (string.Equals(old_ptmlist, new_ptmlist))
{
File.Delete(new_ptmlist_filepath);
}
else
{
File.Delete(old_ptmlist_filepath);
File.Move(new_ptmlist_filepath, old_ptmlist_filepath);
}
}
catch
{
}
XmlDocument psi_mod_temp = new XmlDocument();
psi_mod_temp.Load(Path.Combine(Path.GetDirectoryName(Environment.GetCommandLineArgs()[0]), "PSI-MOD.obo.xml"));
XPathNavigator psi_mod = psi_mod_temp.CreateNavigator();
using (StreamReader uniprot_mods = new StreamReader(old_ptmlist_filepath))
{
string description = null;
string feature_type = null;
ModificationType modification_type = ModificationType.AminoAcidResidue;
char amino_acid_residue = '\0';
double monoisotopic_mass_shift = double.NaN;
double average_mass_shift = double.NaN;
string database = null;
int database_accession_number = -1;
string database_name = null;
while (uniprot_mods.Peek() != -1)
{
string line = uniprot_mods.ReadLine();
if (line.Length >= 2)
{
switch (line.Substring(0, 2))
{
case "ID":
description = line.Substring(5);
break;
case "FT":
feature_type = line.Substring(5);
break;
case "TG":
if (feature_type == "MOD_RES")
{
string amino_acid = line.Substring(5);
aminoAcidCodes.TryGetValue(char.ToUpperInvariant(amino_acid[0]) + amino_acid.Substring(1).TrimEnd('.'), out amino_acid_residue);
}
break;
case "PP":
if (feature_type == "MOD_RES")
{
modificationTypeCodes.TryGetValue(line.Substring(5), out modification_type);
}
break;
case "MM":
monoisotopic_mass_shift = double.Parse(line.Substring(5));
break;
case "MA":
average_mass_shift = double.Parse(line.Substring(5));
break;
case "DR":
if (line.Contains("PSI-MOD"))
{
Match match = PSI_MOD_ACCESSION_NUMBER_REGEX.Match(line.Substring(5));
if (match.Success)
{
database = match.Groups[1].Value;
database_accession_number = int.Parse(match.Groups[2].Value);
XPathNavigator term = psi_mod.SelectSingleNode(@"/obo/term[id='MOD:" + database_accession_number.ToString("00000") + "']");
database_name = term.SelectSingleNode("name").Value;
}
}
break;
case "//":
if (feature_type == "MOD_RES" && modifications_in_database.Contains(description) && (!double.IsNaN(monoisotopic_mass_shift) || !double.IsNaN(average_mass_shift)))
{
Modification modification = new Modification("UniProt: " + description, ModificationType.AminoAcidResidue, amino_acid_residue, monoisotopic_mass_shift, average_mass_shift, 0.0, 0.0, false, true, database, database_accession_number, database_name, true);
modifications.Add(modification.Description, modification);
}
description = null;
feature_type = null;
modification_type = ModificationType.AminoAcidResidue;
amino_acid_residue = '\0';
monoisotopic_mass_shift = double.NaN;
average_mass_shift = double.NaN;
break;
}
}
}
}
}
return(modifications);
}
static void Main(string[] args)
{
if (args.Length > 0)
{
Arguments arguments = new Arguments(args);
List <string> data = new List <string>(arguments["d"].Split(','));
int min_assumed_precursor_charge_state = 2;
if (arguments["minprecz"] != null)
{
min_assumed_precursor_charge_state = int.Parse(arguments["minprecz"]);
}
int max_assumed_precursor_charge_state = 4;
if (arguments["maxprecz"] != null)
{
max_assumed_precursor_charge_state = int.Parse(arguments["maxprecz"]);
}
double abs_threshold = -1.0;
if (arguments["at"] != null)
{
abs_threshold = double.Parse(arguments["at"], CultureInfo.InvariantCulture);
}
double rel_threshold_percent = -1.0;
if (arguments["rt"] != null)
{
rel_threshold_percent = double.Parse(arguments["rt"], CultureInfo.InvariantCulture);
}
int max_peaks = 400;
if (arguments["mp"] != null)
{
max_peaks = int.Parse(arguments["mp"]);
}
bool assign_charge_states = true;
if (arguments["acs"] != null)
{
assign_charge_states = bool.Parse(arguments["acs"]);
}
bool deisotope = true;
if (arguments["di"] != null)
{
deisotope = bool.Parse(arguments["di"]);
}
string database = arguments["db"];
Dictionary <string, Modification> known_variable_modifications = null;
HashSet <Modification> variable_mods = new HashSet <Modification>();
if (Path.GetExtension(database).Equals(".xml", StringComparison.InvariantCultureIgnoreCase))
{
bool no_uniprot_mods = false;
if (arguments["noup"] != null)
{
no_uniprot_mods = bool.Parse(arguments["noup"]);
}
if (!no_uniprot_mods)
{
known_variable_modifications = ProteomeDatabaseReader.ReadUniProtXmlModifications(database);
variable_mods.UnionWith(known_variable_modifications.Values);
}
}
bool append_decoys = false;
if (arguments["ad"] != null)
{
append_decoys = bool.Parse(arguments["ad"]);
}
else
{
append_decoys = Path.GetExtension(database).Equals(".xml", StringComparison.InvariantCultureIgnoreCase) || !ProteomeDatabaseReader.HasDecoyProteins(database);
}
ProteaseDictionary proteases = ProteaseDictionary.Instance;
Protease protease = proteases["trypsin (no proline rule)"];
if (arguments["p"] != null)
{
protease = proteases[arguments["p"]];
}
int max_missed_cleavages = 2;
if (arguments["mmc"] != null)
{
max_missed_cleavages = int.Parse(arguments["mmc"]);
}
InitiatorMethionineBehavior initiator_methionine_behavior = InitiatorMethionineBehavior.Variable;
if (arguments["imb"] != null)
{
initiator_methionine_behavior = (InitiatorMethionineBehavior)Enum.Parse(typeof(InitiatorMethionineBehavior), arguments["imb"], true);
}
ModificationDictionary mods = ModificationDictionary.Instance;
List <Modification> fixed_mods = new List <Modification>();
if (arguments["fm"] != null)
{
foreach (string fixed_mod in arguments["fm"].Split(';'))
{
fixed_mods.Add(mods[fixed_mod]);
}
}
if (arguments["vm"] != null)
{
foreach (string variable_mod in arguments["vm"].Split(';'))
{
Modification mod;
if (!mods.TryGetValue(variable_mod, out mod))
{
known_variable_modifications.TryGetValue(variable_mod, out mod);
}
variable_mods.Add(mod);
}
}
int max_variable_mod_isoforms_per_peptide = 1024;
if (arguments["mvmi"] != null)
{
max_variable_mod_isoforms_per_peptide = int.Parse(arguments["mvmi"]);
}
double precursor_mass_tolerance_value = 2.1;
if (arguments["precmtv"] != null)
{
precursor_mass_tolerance_value = double.Parse(arguments["precmtv"], CultureInfo.InvariantCulture);
}
MassToleranceUnits precursor_mass_tolerance_units = MassToleranceUnits.Da;
if (arguments["precmtu"] != null)
{
precursor_mass_tolerance_units = (MassToleranceUnits)Enum.Parse(typeof(MassToleranceUnits), arguments["precmtu"], true);
}
MassTolerance precursor_mass_tolerance = new MassTolerance(precursor_mass_tolerance_value, precursor_mass_tolerance_units);
MassType precursor_mass_type = MassType.Monoisotopic;
if (arguments["precmt"] != null)
{
precursor_mass_type = (MassType)Enum.Parse(typeof(MassType), arguments["precmt"], true);
}
List <double> accepted_precursor_mass_errors = new List <double>();
if (arguments["apme"] != null && arguments["apme"].Length > 0)
{
foreach (string accepted_precursor_mass_error in arguments["apme"].Split(';'))
{
accepted_precursor_mass_errors.Add(double.Parse(accepted_precursor_mass_error, CultureInfo.InvariantCulture));
}
}
else
{
accepted_precursor_mass_errors.Add(0.0);
}
double product_mass_tolerance_value = 0.015;
if (arguments["prodmtv"] != null)
{
product_mass_tolerance_value = double.Parse(arguments["prodmtv"], CultureInfo.InvariantCulture);
}
MassToleranceUnits product_mass_tolerance_units = MassToleranceUnits.Da;
if (arguments["prodmtu"] != null)
{
product_mass_tolerance_units = (MassToleranceUnits)Enum.Parse(typeof(MassToleranceUnits), arguments["prodmtu"], true);
}
MassTolerance product_mass_tolerance = new MassTolerance(product_mass_tolerance_value, product_mass_tolerance_units);
MassType product_mass_type = MassType.Monoisotopic;
if (arguments["prodmt"] != null)
{
product_mass_type = (MassType)Enum.Parse(typeof(MassType), arguments["prodmt"], true);
}
double max_fdr = 0.01;
if (arguments["fdr"] != null)
{
max_fdr = double.Parse(arguments["fdr"], CultureInfo.InvariantCulture) / 100.0;
}
bool consider_mods_unique = false;
if (arguments["cmu"] != null)
{
consider_mods_unique = bool.Parse(arguments["cmu"]);
}
int max_threads = Environment.ProcessorCount;
if (arguments["mt"] != null)
{
max_threads = int.Parse(arguments["mt"]);
}
bool minimize_memory_usage = false;
if (arguments["mmu"] != null)
{
minimize_memory_usage = bool.Parse(arguments["mmu"]);
}
string output_folder = Environment.CurrentDirectory;
if (arguments["o"] != null)
{
output_folder = arguments["o"];
}
DatabaseSearcher database_searcher = new DatabaseSearcher(data,
min_assumed_precursor_charge_state, max_assumed_precursor_charge_state,
abs_threshold, rel_threshold_percent, max_peaks,
assign_charge_states, deisotope,
database, append_decoys,
protease, max_missed_cleavages, initiator_methionine_behavior,
fixed_mods, variable_mods, max_variable_mod_isoforms_per_peptide,
precursor_mass_tolerance, precursor_mass_type,
accepted_precursor_mass_errors,
product_mass_tolerance, product_mass_type,
max_fdr, consider_mods_unique,
max_threads, minimize_memory_usage,
output_folder);
database_searcher.Starting += HandleStarting;
database_searcher.StartingFile += HandleStartingFile;
database_searcher.UpdateStatus += HandleUpdateStatus;
database_searcher.UpdateProgress += HandleUpdateProgress;
database_searcher.ThrowException += HandleThrowException;
database_searcher.FinishedFile += HandleFinishedFile;
database_searcher.Finished += HandleFinished;
database_searcher.Search();
}
else
{
Console.WriteLine(Program.GetProductNameAndVersion() + " USAGE");
}
}
private void frmMain_Load(object sender, EventArgs e)
{
Text = Program.GetProductNameAndVersion();
label1.Text = FORM_LABEL;
ofdData.Filter = DIALOG_FILTER;
ofdFasta.Filter = Environment.OSVersion.Platform == PlatformID.Unix
? "FASTA proteome database files (" + CASE_INSENSITIVE_FASTA_EXTENSIONS + ")|" + CASE_SENSITIVE_FASTA_EXTENSIONS + "|UniProt XML proteome database files (*.xml)|*.xml;*.XML"
: "FASTA proteome database files|" + CASE_INSENSITIVE_FASTA_EXTENSIONS + "|UniProt XML proteome database files|*.xml";
if (Application.ProductName.Contains("Thermo"))
{
chkDeisotope.Enabled = false;
chkDeisotope.Checked = false;
}
ProteaseDictionary proteases = null;
try
{
proteases = ProteaseDictionary.Instance;
foreach (Protease protease in proteases.Values)
{
cboProtease.Items.Add(protease);
}
}
catch
{
MessageBox.Show("Your proteases file (" + Path.Combine(Path.GetDirectoryName(Environment.GetCommandLineArgs()[0]), "proteases.tsv") + ") is likely corrupt. Please correct it. Program will now exit.");
Application.Exit();
}
foreach (string initiatior_methionine_behavior in Enum.GetNames(typeof(InitiatorMethionineBehavior)))
{
cboInitiatorMethionineBehavior.Items.Add(initiatior_methionine_behavior.ToLower());
}
ModificationDictionary modifications = null;
try
{
modifications = ModificationDictionary.Instance;
clbFixedModifications.BeginUpdate();
clbVariableModifications.BeginUpdate();
foreach (Modification modification in modifications.Values)
{
clbFixedModifications.Items.Add(modification, modification.DefaultFixed);
clbVariableModifications.Items.Add(modification, modification.DefaultVariable);
}
clbFixedModifications.EndUpdate();
clbVariableModifications.EndUpdate();
}
catch
{
MessageBox.Show("Your modifications file (" + Path.Combine(Path.GetDirectoryName(Environment.GetCommandLineArgs()[0]), "modifications.tsv") + ") is likely corrupt. Please correct it.");
}
cboPrecursorMassToleranceUnits.Items.AddRange(Enum.GetNames(typeof(MassToleranceUnits)));
cboProductMassToleranceUnits.Items.AddRange(Enum.GetNames(typeof(MassToleranceUnits)));
foreach (string mass_type in Enum.GetNames(typeof(MassType)))
{
cboPrecursorMassType.Items.Add(mass_type.ToLower());
cboProductMassType.Items.Add(mass_type.ToLower());
}
numMaxThreads.Maximum = Environment.ProcessorCount;
string settings_filepath = Path.Combine(Application.UserAppDataPath, "settings.tsv");
if (File.Exists(settings_filepath))
{
try
{
using (StreamReader settings = new StreamReader(settings_filepath))
{
while (settings.Peek() != -1)
{
string line = settings.ReadLine();
string[] fields = line.Split('\t');
string name = fields[0];
string value = fields[1];
string[] value_fields;
switch (name)
{
case "Minimum Assumed Precursor Charge State":
numMinimumAssumedPrecursorChargeState.Value = int.Parse(value);
break;
case "Maximum Assumed Precursor Charge State":
numMaximumAssumedPrecursorChargeState.Value = int.Parse(value);
break;
case "Absolute MS/MS Peak Threshold":
value_fields = value.Split(';');
chkAbsoluteThreshold.Checked = bool.Parse(value_fields[0]);
txtAbsoluteThreshold.Text = value_fields[1];
break;
case "Relative MS/MS Peak Threshold (%)":
value_fields = value.Split(';');
chkRelativeThreshold.Checked = bool.Parse(value_fields[0]);
txtRelativeThresholdPercent.Text = value_fields[1];
break;
case "Maximum Number of MS/MS Peaks":
value_fields = value.Split(';');
chkMaxNumPeaks.Checked = bool.Parse(value_fields[0]);
numMaxPeaks.Value = int.Parse(value_fields[1]);
break;
case "Assign Charge States":
chkAssignChargeStates.Checked = bool.Parse(value);
break;
case "De-isotope":
if (!Application.ProductName.Contains("Thermo"))
{
chkDeisotope.Checked = bool.Parse(value);
}
break;
case "Protease":
cboProtease.SelectedItem = proteases[value];
break;
case "Maximum Missed Cleavages":
numMaxMissedCleavages.Value = int.Parse(value);
break;
case "Initiator Methionine Behavior":
cboInitiatorMethionineBehavior.SelectedIndex = (int)Enum.Parse(typeof(InitiatorMethionineBehavior), value, true);
break;
case "Maximum Variable Modification Isoforms per Peptide":
numMaxVariableModIsoforms.Value = int.Parse(value);
break;
case "Precursor Mass Tolerance":
numPrecursorMassTolerance.Value = decimal.Parse(value, CultureInfo.InvariantCulture);
break;
case "Precursor Mass Tolerance Units":
cboPrecursorMassToleranceUnits.SelectedIndex = (int)Enum.Parse(typeof(MassToleranceUnits), value, true);
break;
case "Precursor Mass Type":
cboPrecursorMassType.SelectedIndex = (int)Enum.Parse(typeof(MassType), value, true);
break;
case "Accepted Precursor Mass Errors (Da)":
txtAcceptedPrecursorMassErrors.Text = value;
break;
case "Product Mass Tolerance":
numProductMassTolerance.Value = decimal.Parse(value, CultureInfo.InvariantCulture);
break;
case "Product Mass Tolerance Units":
cboProductMassToleranceUnits.SelectedIndex = (int)Enum.Parse(typeof(MassToleranceUnits), value, true);
break;
case "Product Mass Type":
cboProductMassType.SelectedIndex = (int)Enum.Parse(typeof(MassType), value, true);
break;
case "Maximum FDR (%)":
numMaximumFalseDiscoveryRatePercent.Value = decimal.Parse(value, CultureInfo.InvariantCulture);
break;
case "Consider Modified Forms as Unique Peptides":
chkConsiderModifiedUnique.Checked = bool.Parse(value);
break;
case "Maximum Threads":
if (int.Parse(value) > numMaxThreads.Maximum)
{
numMaxThreads.Value = numMaxThreads.Maximum;
}
else
{
numMaxThreads.Value = int.Parse(value);
}
break;
case "Minimize Memory Usage":
chkMinimizeMemoryUsage.Checked = bool.Parse(value);
break;
}
}
}
return;
}
catch
{
MessageBox.Show("Your settings file (" + settings_filepath + ") is likely corrupt. Defaults will be used.");
}
}
cboProtease.SelectedItem = proteases["trypsin (no proline rule)"];
cboInitiatorMethionineBehavior.SelectedIndex = (int)InitiatorMethionineBehavior.Variable;
cboPrecursorMassToleranceUnits.SelectedIndex = (int)MassToleranceUnits.Da;
cboPrecursorMassType.SelectedIndex = (int)MassType.Monoisotopic;
cboProductMassToleranceUnits.SelectedIndex = (int)MassToleranceUnits.Da;
cboProductMassType.SelectedIndex = (int)MassType.Monoisotopic;
numMaxThreads.Value = numMaxThreads.Maximum;
}
