//generate pIsobariQ.cfg
void pQuant_Inter.pIsobariQ_write(_Task _task)
{
try
{
MS2Quant _ms2quant = _task.T_MS2Quant;
File _file = _task.T_File;
string filepath = _task.Path + "param\\pIsobariQ.cfg";
FileStream qfst = new FileStream(filepath, FileMode.Create, FileAccess.Write);
StreamWriter qsw = new StreamWriter(qfst, Encoding.Default);
qsw.WriteLine("# This is a standard pIsobariQ configure file.");
qsw.WriteLine("# For help: mail to [email protected]");
qsw.WriteLine("# Time: " + DateTime.Now.ToString());
qsw.WriteLine();
qsw.WriteLine("[Basic Options]");
qsw.WriteLine("resultDatapath=" + _task.Path + "result\\pFind.spectra");
string pf1path = "";
for (int i = 0; i < _file.Data_file_list.Count; i++)
{
string tmp = _file.Data_file_list[i].FilePath;
pf1path += tmp.Substring(0, tmp.LastIndexOf(".")) + ".pf1|";
}
// 这里我只给出了所有pf1的路径，内核可以自动切割字符串并查找相关的pf2的路径
qsw.WriteLine("pfDatapath=" + pf1path);
qsw.WriteLine("quantResultDatapath=" + _task.Path + "result\\pQuant-ms2_result.spectra");
qsw.WriteLine();
qsw.WriteLine("[Database Options]");
qsw.WriteLine("fastaDatapath=" + _task.T_Search.Db.Db_path);
qsw.WriteLine("modificationDatapath=" + ConfigHelper.startup_path + "\\modification.ini");
qsw.WriteLine();
qsw.WriteLine("[Method Options]");
qsw.WriteLine("quantitativeMethod=" + _task.T_MS2Quant.QuantitativeMethod);
string tmpstr = "";
if (_task.T_MS2Quant.ReporterIonMZ.Count > 0)
{
tmpstr += _task.T_MS2Quant.ReporterIonMZ[0].ToString();
}
for (int i = 1; i < _task.T_MS2Quant.ReporterIonMZ.Count; ++i)
{
tmpstr += ", " + _task.T_MS2Quant.ReporterIonMZ[i].ToString();
}
qsw.WriteLine("reporterIonMZ=" + tmpstr);
tmpstr = "";
if (_task.T_MS2Quant.PIDL.Count > 0)
{
tmpstr += _task.T_MS2Quant.PIDL[0].Nterm_modmass.Name + " " + _task.T_MS2Quant.PIDL[0].Nterm_modmass.Mass.ToString() + ", ";
tmpstr += _task.T_MS2Quant.PIDL[0].Cterm_modmass.Name + " " + _task.T_MS2Quant.PIDL[0].Cterm_modmass.Mass.ToString();
}
for (int i = 1; i < _task.T_MS2Quant.PIDL.Count; ++i)
{
tmpstr += "; " + _task.T_MS2Quant.PIDL[i].Nterm_modmass.Name + " " + _task.T_MS2Quant.PIDL[i].Nterm_modmass.Mass.ToString() + ", ";
tmpstr += _task.T_MS2Quant.PIDL[i].Cterm_modmass.Name + " " + _task.T_MS2Quant.PIDL[i].Cterm_modmass.Mass.ToString();
}
qsw.WriteLine("pIDLplex=" + tmpstr);
qsw.WriteLine();
qsw.WriteLine("[Advanced Options]");
qsw.WriteLine("FTMSType=" + ((_task.T_MS2Quant.MS2_Advanced.FTMS_Tolerance.Isppm == 1) ? "ppm":"Da"));
qsw.WriteLine("FTMS=" + _task.T_MS2Quant.MS2_Advanced.FTMS_Tolerance.Tl_value.ToString());
qsw.WriteLine("minRange=" + _task.T_MS2Quant.MS2_Advanced.Peak_Range.Left_value.ToString());
qsw.WriteLine("maxRange=" + _task.T_MS2Quant.MS2_Advanced.Peak_Range.Right_value.ToString());
qsw.WriteLine("PIF=" + _task.T_MS2Quant.MS2_Advanced.Pif.ToString());
qsw.WriteLine("PsmFDR=" + (_task.T_MS2Quant.MS2_Advanced.Psm_Fdr / 100.0).ToString());
qsw.WriteLine("ProteinFDR=" + (_task.T_MS2Quant.MS2_Advanced.Protein_Fdr / 100.0).ToString());
qsw.WriteLine("Correct=" + (_task.T_MS2Quant.MS2_Advanced.Correct ? "1":"0"));
qsw.WriteLine("runVSN=" + (_task.T_MS2Quant.MS2_Advanced.RunVSN ? "1":"0"));
qsw.WriteLine();
qsw.Close();
qfst.Close();
}
catch (Exception exe)
{
throw new Exception("[pIsobariQ_write] Error in pIsobariQ configuration file.\n" + exe.Message);
}
}
//read from pIsobariQ param
void pQuant_Inter.pIsobariQ_read(string task_path, ref _Task _task)
{
try
{
FileStream fst = new FileStream(task_path + "\\param\\pIsobariQ.cfg", FileMode.Open);
StreamReader sr = new StreamReader(fst, Encoding.Default);
string strLine = sr.ReadLine();
#region
MS2Quant _ms2quant = _task.T_MS2Quant;
while (strLine != null)
{
strLine = strLine.Trim();
if (strLine.Length > 0 && strLine.Contains("="))
{
if (strLine.Length > ("quantitativeMethod").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("quantitativeMethod"))
{
int tmp = strLine.LastIndexOf("=");
_ms2quant.QuantitativeMethod = int.Parse(strLine.Substring(tmp + 1));
}
else if (strLine.Length > ("reporterIonMZ").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("reporterIonMZ"))
{
int tmp = strLine.LastIndexOf("=");
string tmpstr = strLine.Substring(tmp + 1);
string[] tmparray = tmpstr.Split(new string[] { ", " }, StringSplitOptions.RemoveEmptyEntries);
foreach (string str in tmparray)
{
_ms2quant.ReporterIonMZ.Add(double.Parse(str));
}
}
else if (strLine.Length > ("pIDLplex").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("pIDLplex"))
{
int tmp = strLine.LastIndexOf("=");
string tmpstr = strLine.Substring(tmp + 1);
string[] tmparray = tmpstr.Split(new string[] { "; " }, StringSplitOptions.RemoveEmptyEntries);
foreach (string str in tmparray)
{
string[] modmass = str.Split(new string[] { ", " }, StringSplitOptions.RemoveEmptyEntries);
if (modmass.Length != 2)
{
continue;
}
string[] nterm = modmass[0].Split(new Char[] { ' ' }, StringSplitOptions.RemoveEmptyEntries);
string[] cterm = modmass[1].Split(new Char[] { ' ' }, StringSplitOptions.RemoveEmptyEntries);
if (nterm.Length != 2 || cterm.Length != 2)
{
continue;
}
_ms2quant.PIDL.Add(new pIDLplex(nterm[0], double.Parse(nterm[1]), cterm[0], double.Parse(cterm[1])));
}
}
else if (strLine.Length > ("FTMSType").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("FTMSType"))
{
int tmp = strLine.LastIndexOf("=");
string ftoltype = strLine.Substring(tmp + 1);
if (ftoltype.ToLower() == "da")
{
_ms2quant.MS2_Advanced.FTMS_Tolerance.Isppm = 0;
}
else if (ftoltype.ToLower() == "ppm")
{
_ms2quant.MS2_Advanced.FTMS_Tolerance.Isppm = 1;
}
}
else if (strLine.Length > ("FTMS").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("FTMS"))
{
int tmp = strLine.LastIndexOf("=");
_ms2quant.MS2_Advanced.FTMS_Tolerance.Tl_value = double.Parse(strLine.Substring(tmp + 1));
}
else if (strLine.Length > ("minRange").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("minRange"))
{
int tmp = strLine.LastIndexOf("=");
_ms2quant.MS2_Advanced.Peak_Range.Left_value = double.Parse(strLine.Substring(tmp + 1));
}
else if (strLine.Length > ("maxRange").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("maxRange"))
{
int tmp = strLine.LastIndexOf("=");
_ms2quant.MS2_Advanced.Peak_Range.Right_value = double.Parse(strLine.Substring(tmp + 1));
}
else if (strLine.Length > ("PIF").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("PIF"))
{
int tmp = strLine.LastIndexOf("=");
_ms2quant.MS2_Advanced.Pif = double.Parse(strLine.Substring(tmp + 1));
}
else if (strLine.Length > ("PsmFDR").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("PsmFDR"))
{
int tmp = strLine.LastIndexOf("=");
_ms2quant.MS2_Advanced.Psm_Fdr = double.Parse(strLine.Substring(tmp + 1)) * 100;
}
else if (strLine.Length > ("ProteinFDR").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("ProteinFDR"))
{
int tmp = strLine.LastIndexOf("=");
_ms2quant.MS2_Advanced.Protein_Fdr = double.Parse(strLine.Substring(tmp + 1)) * 100;
}
else if (strLine.Length > ("Correct").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("Correct"))
{
int tmp = strLine.LastIndexOf("=");
_ms2quant.MS2_Advanced.Correct = (int.Parse(strLine.Substring(tmp + 1)) == 1) ? true : false;
}
else if (strLine.Length > ("runVSN").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("runVSN"))
{
int tmp = strLine.LastIndexOf("=");
_ms2quant.MS2_Advanced.RunVSN = (int.Parse(strLine.Substring(tmp + 1)) == 1) ? true : false;
}
}
strLine = sr.ReadLine();
}
#endregion
sr.Close();
fst.Close();
}
catch (Exception exe)
{
throw new Exception("[pIsobariQ_read] Error in pIsobariQ configuration file.\n" + exe.Message);
}
}
