private void buttonGenerateCommetParams_Click(object sender, EventArgs e)
{
cometParams cp = GetCometParamsFromScreen();
try
{
CheckForConsistencyInForms(cp);
}
catch (Exception e3)
{
MessageBox.Show(e3.Message);
return;
}
string cpf = GenerateTheSearchParamsString(cp);
//Serialize it and check if it is different than the default parameters
//If it is different, we ask the user if the default parameters should be updated
string serializedCometParams = cp.SerializeToXML();
if (!serializedCometParams.Equals(Properties.Settings.Default.SearchSettings))
{
if (MessageBox.Show("Update default search parameters ?", "Default parameters", MessageBoxButtons.YesNo) == DialogResult.Yes)
{
Settings.Default.SearchSettings = serializedCometParams;
Settings.Default.Save();
}
}
richTextBoxVerify.Text = cpf;
tabControl1.SelectedTab = tabPageVerify;
}
public static List <SQTScan2> CallComet(cometParams cp, string searchFile)
{
FileInfo fi = new FileInfo(searchFile);
string cpf = CometWrapper.GenerateTheSearchParamsString(cp);
//Write the comet result to the directory
StreamWriter sw = new StreamWriter(fi.DirectoryName + "/" + "comet.params");
sw.WriteLine(cpf);
sw.Close();
string cometCall = CometWrapper.GetCometPath();
CometWrapper.CallComet(fi, cometCall, cpf);
string sqtFileTmp = fi.Name.Replace(fi.Extension, ".sqt");
string sqtFile = fi.Directory.FullName + "/" + sqtFileTmp;
PatternTools.SQTParser2.SQTParser2 sqtParser = new SQTParser2();
List <SQTScan2> theResult = sqtParser.Parse(sqtFile);
int removedNoMatch = theResult.RemoveAll(a => a.Matches.Count == 0);
return(theResult);
}
private void CometWrapper_Load(object sender, EventArgs e)
{
comboBoxEnzyme.DataSource = enzymes;
comboBoxEnzyme.SelectedIndex = 1;
comboBoxEnzymeSpecificity.SelectedIndex = 0;
comboBoxTheoreticalFragIons.SelectedIndex = 0;
Control.CheckForIllegalCrossThreadCalls = false;
//Load Default search Parameters
try
{
cometParams cp = new cometParams();
StringReader s = new StringReader(Properties.Settings.Default.SearchSettings);
XmlSerializer xmlSerializer = new XmlSerializer(cp.GetType());
cp = (cometParams)xmlSerializer.Deserialize(s);
//Now we need to update the screen
UpdateScreenFromSerializedObject(cp);
}
catch (Exception e4)
{
MessageBox.Show("No default parameters have been set.\n" + e4.Message);
}
}
//--------------------------------------------------------
private void CheckForConsistencyInForms(cometParams cp)
{
Console.WriteLine("Checking for consistency in forms.");
if (!Directory.Exists(textBoxInput.Text))
{
throw new Exception("Please enter a valid input directory containing .RAW, .mgf, .ms2, or .mzML files");
}
List <string> searchDirs = GetDirectoriesWithRawOrMS2orMZMLorMGF();
if (searchDirs.Count == 0)
{
throw new Exception("No .RAW, .mgf, .mzXML, .ms2, or mzML files found for searching.");
}
//Verify if we have a comet.params in all directories
List <string> directories = GetDirectoriesWithRawOrMS2orMZMLorMGF();
//Verify if we have a valid search sequence database
if (!File.Exists(textBoxSequenceDatabase.Text))
{
throw new Exception("No sequence database file found.");
}
//Check if at least one ion type is selected
if (checkBoxIon_B.Checked && checkBoxIon_X.Checked && checkBoxIonA.Checked && checkBoxIonC.Checked && checkBoxIonNL.Checked && checkBoxIonY.Checked && checkBoxIonZ.Checked)
{
throw new Exception("At lease one ion type must be selected");
}
if (numericUpDownClearMZMin.Value > numericUpDownClearMZMax.Value)
{
throw new Exception("Clear MZ Min value must be less than Clear MZ Max value.");
}
if (numericUpDownSearchMassMin.Value > numericUpDownSearchMassMax.Value)
{
throw new Exception("Search mass maximum must be greater than search mass min.");
}
if (cp.MyModificationItems.Count(a => a.isCTerm && !a.isDiff) > 1)
{
throw new Exception("Only one static C terminal modification is allowed");
}
if (cp.MyModificationItems.Count(a => a.isNTerm && !a.isDiff) > 1)
{
throw new Exception("Only one static N terminal modification is allowed");
}
}
//--------------------------------------------
private cometParams GetCometParamsFromScreen()
{
cometParams cp = new cometParams();
cp.SequenceDatabase = textBoxSequenceDatabase.Text;
cp.IonsA = checkBoxIonA.Checked;
cp.IonsB = checkBoxIon_B.Checked;
cp.IonsC = checkBoxIonC.Checked;
cp.IonsX = checkBoxIon_X.Checked;
cp.IonsY = checkBoxIonY.Checked;
cp.IonsZ = checkBoxIonZ.Checked;
cp.IonsNL = checkBoxIonNL.Checked;
cp.PrecursorMassTolerance = (double)numericUpDownPrecursorMassTolerance.Value;
cp.Enzyme = comboBoxEnzyme.SelectedIndex;
cp.EnzymeSpecificity = comboBoxEnzymeSpecificity.SelectedIndex + 1;
cp.MissedCleavages = (int)numericUpDownAllowedMissedCleavages.Value;
cp.FragmentBinTolerance = (double)numericUpDownFragmentBinTolerance.Value;
cp.FragmentBinOffset = (double)numericUpDownFragBinOffset.Value;
if ((int)comboBoxTheoreticalFragIons.SelectedIndex == 0)
{
cp.TheoreticalFragIons = 1;
}
else
{
cp.TheoreticalFragIons = 0;
}
cp.MaxVariableModsPerPeptide = (int)numericUpDownMaxVariableModsPerPeptides.Value;
cp.ClearMZRangeMin = (double)numericUpDownClearMZMin.Value;
cp.ClearMZRangeMax = (double)numericUpDownClearMZMax.Value;
cp.SearchMassRangeMin = (double)numericUpDownSearchMassMin.Value;
cp.SearchMassRangeMax = (double)numericUpDownSearchMassMax.Value;
cp.MyModificationItems = GetModsFromTable();
return(cp);
}
static void Main(string[] args)
{
int minNoPeptides = 2;
double minAcceptableXCorr = 1.7;
string sequenceDB = @"C:\Users\pcarvalho\Desktop\XIC\BSA\PFUsmall.T-R";
string massSpectraFile = @"C:\Users\pcarvalho\Desktop\XIC\BSA\1\20111024_BSA_40fmol_01.RAW";
CometWrapper.cometParams cp = new CometWrapper.cometParams();
cp.ClearMZRangeMax = 0;
cp.ClearMZRangeMin = 0;
cp.Enzyme = 1; //Trypsin
cp.EnzymeSpecificity = 2;
cp.FragmentBinOffset = 0.4;
cp.FragmentBinTolerance = 1.0005;
cp.IonsA = false;
cp.IonsB = true;
cp.IonsC = false;
cp.IonsNL = true;
cp.IonsX = false;
cp.IonsY = true;
cp.IonsZ = false;
cp.MaxVariableModsPerPeptide = 3;
cp.MissedCleavages = 4;
Modification m1 = new Modification("Carb", (decimal)57.02146, "C");
//Modification m2 = new Modification("M", (decimal)15.9949, "M");
//m2.isDiff = true;
//For cross-linker dead end, include as a variable mod, and then as a variable mod for n-terminal
cp.MyModificationItems = new List <CometWrapper.Modification>()
{
m1
};
cp.PrecursorMassTolerance = 40;
cp.SearchMassRangeMax = 5500;
cp.SearchMassRangeMin = 550;
cp.SequenceDatabase = sequenceDB;
cp.TheoreticalFragIons = 1;
List <SQTScan2> myResults = CometWrapper.RemoteCall.CallComet(cp, massSpectraFile);
int removedPrimary = myResults.RemoveAll(a => a.Matches[0].PrimaryScore < minAcceptableXCorr);
var proteinIDs = (from result in myResults
from ID id in result.Matches[0].IDs
group id by id.Locus into myLocusGroups
select new { ID = myLocusGroups.Key, Count = myLocusGroups.Count() });
List <string> peptides = (from result in myResults
select result.Matches[0].PeptideSequence).Distinct().ToList();
PatternTools.FastaParser.FastaFileParser ffp = new PatternTools.FastaParser.FastaFileParser();
ffp.ParseFile(new StreamReader(cp.SequenceDatabase), true, PatternTools.FastaParser.DBTypes.IDSpaceDescription);
List <FastaItem> myFasta = new List <FastaItem>();
foreach (var prot in proteinIDs)
{
if (prot.Count >= minNoPeptides)
{
myFasta.Add(ffp.MyItems.Find(a => a.SequenceIdentifier.Equals(prot.ID)));
}
}
Console.WriteLine("Done");
}
public static string GenerateTheSearchParamsString(cometParams cp)
{
string cpt = Properties.Settings.Default.CometParamsTemplate;
cpt = cpt.Replace("[CLEARMZRANGEMAX]", cp.ClearMZRangeMax.ToString());
cpt = cpt.Replace("[CLEARMZRANGEMIN]", cp.ClearMZRangeMin.ToString());
cpt = cpt.Replace("[ENZYME]", cp.Enzyme.ToString());
cpt = cpt.Replace("[SAMPLENZYME]", cp.Enzyme.ToString());
cpt = cpt.Replace("[DIGESTIONSPECIFICITY]", cp.EnzymeSpecificity.ToString());
cpt = cpt.Replace("[FRAGMENTBINOFFSET]", cp.FragmentBinOffset.ToString());
cpt = cpt.Replace("[FRAGMENTBINTOLERANCE]", cp.FragmentBinTolerance.ToString());
cpt = cpt.Replace("[A_ION]", BoolHelper(cp.IonsA));
cpt = cpt.Replace("[B_ION]", BoolHelper(cp.IonsB));
cpt = cpt.Replace("[C_ION]", BoolHelper(cp.IonsC));
cpt = cpt.Replace("[NL_ION]", BoolHelper(cp.IonsNL));
cpt = cpt.Replace("[X_ION]", BoolHelper(cp.IonsX));
cpt = cpt.Replace("[Y_ION]", BoolHelper(cp.IonsY));
cpt = cpt.Replace("[Z_ION]", BoolHelper(cp.IonsZ));
cpt = cpt.Replace("[MAXVARIABLEMODSPERPEPTIDE]", cp.MaxVariableModsPerPeptide.ToString());
cpt = cpt.Replace("[MISSEDCLEAVAGES]", cp.MissedCleavages.ToString());
cpt = cpt.Replace("[PEPTIDEMASSTOLERANCE]", cp.PrecursorMassTolerance.ToString());
cpt = cpt.Replace("[MASSRANGEMAX]", cp.SearchMassRangeMax.ToString());
cpt = cpt.Replace("[MASSRANGEMIN]", cp.SearchMassRangeMin.ToString());
cpt = cpt.Replace("[DBPATH]", cp.SequenceDatabase);
cpt = cpt.Replace("[THEORETICALFRAGMENTIONS]", cp.TheoreticalFragIons.ToString());
//Static mods for amino acids
List <string> staticModKeys = new List <string>()
{
"[ADD_G]", "[ADD_A]", "[ADD_S]", "[ADD_P]", "[ADD_V]", "[ADD_T]",
"[ADD_C]", "[ADD_L]", "[ADD_I]", "[ADD_N]", "[ADD_D]", "[ADD_Q]",
"[ADD_K]", "[ADD_E]", "[ADD_M]", "[ADD_O]", "[ADD_H]", "[ADD_F]",
"[ADD_R]", "[ADD_Y]", "[ADD_W]", "[ADD_B]", "[ADD_J]", "[ADD_U]",
"[ADD_X]", "[ADD_Z]"
};
List <Modification> staticMod = cp.MyModificationItems.FindAll(a => !a.isDiff);
foreach (string smod in staticModKeys)
{
string[] cols = Regex.Split(smod, "_");
cols[1] = cols[1].Remove(1, 1);
List <Modification> mods = staticMod.FindAll(a => a.Residues.Contains(cols[1]));
foreach (Modification m in mods)
{
cpt = cpt.Replace(smod, m.MassShift.ToString());
}
if (mods.Count == 0)
{
cpt = cpt.Replace(smod, "0.0");
}
}
//Variable mods for amino acids
List <Modification> varMod = cp.MyModificationItems.FindAll(a => a.isDiff);
for (int i = 0; i < 6; i++)
{
int j = i + 1;
if (i < varMod.Count)
{
string res = varMod[i].Residues;
if (varMod[i].isCTerm)
{
res += "c";
}
if (varMod[i].isNTerm)
{
res = "n" + res;
}
cpt = cpt.Replace("[VARMOD" + j + "]", varMod[i].MassShift + " " + res + " 0 4 -1 0 0");
}
else
{
cpt = cpt.Replace("[VARMOD" + j + "]", "0.0 X 0 3 -1 0 0");
}
}
//C static mod
List <Modification> CstaticMod = cp.MyModificationItems.FindAll(a => !a.isDiff && a.isCTerm);
if (CstaticMod.Count > 1)
{
throw new Exception("Only 1 C static mod is acceptable");
}
if (CstaticMod.Count == 1)
{
cpt = cpt.Replace("[FIXEDCTERMINUS]", CstaticMod[0].MassShift.ToString());
}
else
{
cpt = cpt.Replace("[FIXEDCTERMINUS]", "0.0");
}
//N static mod
List <Modification> NstaticMod = cp.MyModificationItems.FindAll(a => !a.isDiff && a.isNTerm);
if (NstaticMod.Count > 1)
{
throw new Exception("Only 1 N static mod is acceptable");
}
if (NstaticMod.Count == 1)
{
cpt = cpt.Replace("[FIXEDNTERMINUS]", NstaticMod[0].MassShift.ToString());
}
else
{
cpt = cpt.Replace("[FIXEDNTERMINUS]", "0.0");
}
return(cpt);
}
