//read from pTop.pfd
void pTop_Inter.pTop_read(string task_path, bool pParse, ref _Task _task)
{
string strLine = "";
try
{
pTop.classes.File _file = _task.T_File;
Identification _search = _task.T_Identify;
Quantitation _quantitation = _task.T_Quantify;
FileStream fst = new FileStream(task_path + "\\param\\pTop.cfg", FileMode.Open);
StreamReader sr = new StreamReader(fst, Encoding.Default);
strLine = sr.ReadLine();
string subtitle = "";
#region
while (strLine != null)
{
strLine = strLine.Trim();
if (strLine.Length > 0 && strLine[0] == '[' && strLine[strLine.Length - 1] == ']')
{
subtitle = strLine;
}
else if (strLine.Length > 0 && strLine.IndexOf("=") > -1)
{
if (subtitle.Equals("[spectrum]"))
{
// msmspath and input_format were read from pParseTD.cfg
if (strLine.Length > ("Activation").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("Activation"))
{
_file.Instrument = strLine.Substring(strLine.LastIndexOf("=") + 1);
_file.setInstrument_index();
}
else if (strLine.Length > ("Precursor_Tolerance").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("Precursor_Tolerance"))
{
_search.Ptl.Tl_value = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > ("Fragment_Tolerance").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("Fragment_Tolerance"))
{
_search.Ftl.Tl_value = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
}
else if (subtitle.Equals("[param]"))
{
if (strLine.Length > ("workflow").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("workflow"))
{
_search.SearchModeIndex = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > ("output_top_k").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("output_top_k"))
{
_search.OutputTopK = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > ("max_truncated_mass").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("max_truncated_mass"))
{
_search.MaxTruncatedMass = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > ("second_search").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("second_search"))
{
if (strLine.Substring(strLine.LastIndexOf("=") + 1).Equals("1"))
{
_search.SecondSearch = true;
}
else
{
_search.SecondSearch = false;
}
}
}
else if (subtitle.Equals("[fixmodify]"))
{
if (strLine.Length > ("fixedModify_num").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("fixedModify_num"))
{
int fix_num = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
_search.Fix_mods.Clear();
for (int i = 0; i < fix_num; i++)
{
strLine = sr.ReadLine();
string fixmod = strLine.Substring(strLine.LastIndexOf("=") + 1);
_search.Fix_mods.Add(fixmod);
}
}
}
else if (subtitle.Equals("[modify]"))
{
if (strLine.Length > ("Max_mod_num").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("Max_mod_num"))
{
_search.Max_mod = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > ("unexpected_mod").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("unexpected_mod"))
{
_search.UnexpectedModNum = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > ("Max_mod_mass").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("Max_mod_mass"))
{
_search.MaxModMass = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
}
else if (strLine.Length > ("Modify_num").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("Modify_num"))
{
int var_num = int.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1));
_search.Var_mods.Clear();
for (int i = 0; i < var_num; i++)
{
strLine = sr.ReadLine();
string varmod = strLine.Substring(strLine.LastIndexOf("=") + 1);
_search.Var_mods.Add(varmod);
}
}
}
else if (subtitle.Equals("[filter]"))
{
if (strLine.Length > ("threshold").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("threshold"))
{
_search.Filter.Fdr_value = double.Parse(strLine.Substring(strLine.LastIndexOf("=") + 1)) * 100;
}
else if (strLine.Length > ("separate_filtering").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("separate_filtering"))
{
if (strLine.Substring(strLine.LastIndexOf("=") + 1).Equals("1"))
{
_search.Filter.SeparateFiltering = true;
}
else
{
_search.Filter.SeparateFiltering = false;
}
}
}
#region [file]
if (subtitle.Equals("[file]"))
{
if (strLine.Length > ("Database").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("Database"))
{
string db_path = strLine.Substring(strLine.LastIndexOf("=") + 1);
if (db_path.Trim().Length > 0)
{
DB db = new DB();
db.Db_path = db_path;
if (ConfigHelper.ReDBmap.Contains(db.Db_path))
{
db.Db_name = ConfigHelper.ReDBmap[db.Db_path].ToString();
_search.Db = db;
_search.Db_index = _search.setDatabaseIndex();
}
else //the database is damaged
{
_search.Db_index = -1;
_search.Db = db;
}
}
else //when new a task
{
_search.Db_index = -1;
_search.Db = new DB();
}
#region Todo
//当不存在指定数据库时
#endregion
}
else if (strLine.Length > ("pParseTD_cfg").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("pParseTD_cfg"))
{
}
else if (strLine.Length > ("pQuant_cfg").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("pQuant_cfg"))
{
}
else if (strLine.Length > ("outputpath").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("outputpath"))
{
string tpath = strLine.Substring(strLine.LastIndexOf("=") + 1);
if (tpath.Trim().Length > 0)
{
if (task_path.EndsWith("\\"))
{
task_path = task_path.Substring(0, task_path.Length - 1);
}
_task.Path = task_path + "\\";
_task.Task_name = task_path.Substring(task_path.LastIndexOf("\\") + 1);
}
}
}
#endregion
else if (subtitle.Equals("[quantify]"))
{
if (strLine.Length > 5 && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("quant"))
{
string qt = strLine.Substring(strLine.LastIndexOf("=") + 1);
string[] lb = qt.Split('|');
int lbcount = lb.GetUpperBound(0);
int lbnum = int.Parse(lb[0]);
#region 如果是MGF文件怎么办
#endregion
//labeling
if (lbnum == 1 && (lb[1].Equals("none") || lb[1].Equals("None")))
{
_quantitation.Quantitation_type = (int)Quant_Type.Label_None;
}
else
{
_quantitation.Quantitation_type = (int)Quant_Type.Labeling; //if 15N, it will be changed in pQuant_Read
_quantitation.Labeling.Multiplicity = lbnum;
_quantitation.Labeling.Multiplicity_index = lbnum - 1;
if (lbnum == 1)
{
/*
* string[] lbs = lb[1].Split(',');
* foreach (string c in lbs)
* {
* if (c.Trim() != ""&&c.ToLower()!="none")
* {
* _quantitation.Labeling.Medium_label.Add(c.Trim());
* }
* }*/
_quantitation.Labeling.Medium_label.Add(lb[1]);
}
else if (lbnum == 2)
{
_quantitation.Labeling.Light_label.Add(lb[1]);
_quantitation.Labeling.Heavy_label.Add(lb[2]);
}
else if (lbnum == 3)
{
_quantitation.Labeling.Light_label.Add(lb[1]);
_quantitation.Labeling.Medium_label.Add(lb[2]);
_quantitation.Labeling.Heavy_label.Add(lb[3]);
}
}
}
}
}
strLine = sr.ReadLine();
}
#endregion
sr.Close();
fst.Close();
}
catch (Exception exe)
{
throw new Exception("[pTop_read] line: " + strLine + "\n" + exe.Message);
}
}
//generate pTop.cfg
void pTop_Inter.pTop_write(_Task _task)
{
try
{
pTop.classes.File _file = _task.T_File;
Identification _search = _task.T_Identify;
Quantitation _quantitation = _task.T_Quantify;
StreamReader sr = new StreamReader(@"pTop.ini", Encoding.Default);
string strLine = sr.ReadLine();
string thread = "";
while (strLine != null)
{
if (strLine.Length > 6 && strLine.Substring(0, 6).Equals("thread"))
{
thread = strLine.Substring(strLine.LastIndexOf("=") + 1);
}
if (thread != "")
{
break;
}
strLine = sr.ReadLine();
}
string filepath = _task.Path + "param\\pTop.cfg";
FileStream pFfst = new FileStream(filepath, FileMode.Create, FileAccess.Write);
StreamWriter pFsw = new StreamWriter(pFfst, Encoding.Default);
pFsw.WriteLine("# This is a standard pTop configuration file");
pFsw.WriteLine("# For help: mail to [email protected]");
pFsw.WriteLine("# Time: " + DateTime.Now.ToString());
pFsw.WriteLine();
pFsw.WriteLine("[Version]");
pFsw.WriteLine("pTop_Version=EVA.2.0");
pFsw.WriteLine();
pFsw.WriteLine("[spectrum]");
pFsw.WriteLine("msmsnum=" + _file.Data_file_list.Count.ToString());
for (int i = 0; i < _file.Data_file_list.Count; i++)
{
string mgfpath = _file.Data_file_list[i].FilePath;
pFsw.WriteLine("msmspath" + (i + 1).ToString() + "=" + mgfpath);
}
pFsw.WriteLine("input_format=" + _file.File_format);
pFsw.WriteLine("Activation=" + _file.Instrument);
//母离子误差指定为 Da
pFsw.WriteLine("Precursor_Tolerance=" + _search.Ptl.Tl_value.ToString());
//pFsw.WriteLine("mstolppm=" + _search.Ptl.Isppm.ToString());
//碎片离子误差指定为 ppm
pFsw.WriteLine("Fragment_Tolerance=" + _search.Ftl.Tl_value.ToString());
//pFsw.WriteLine("msmstolppm=" + _search.Ftl.Isppm.ToString());
pFsw.WriteLine();
pFsw.WriteLine("[param]");
pFsw.WriteLine("thread_num=" + thread);
pFsw.WriteLine("workflow=" + _search.SearchModeIndex.ToString());
pFsw.WriteLine("# 0 tag flow, 1 ion flow");
pFsw.WriteLine("output_top_k=" + _search.OutputTopK.ToString());
pFsw.WriteLine("max_truncated_mass=" + _search.MaxTruncatedMass.ToString());
pFsw.WriteLine("second_search=" + (_search.SecondSearch ? "1" : "0"));
pFsw.WriteLine();
pFsw.WriteLine("[fixmodify]");
pFsw.WriteLine("fixedModify_num=" + _search.Fix_mods.Count.ToString());
for (int i = 0; i < _search.Fix_mods.Count; i++)
{
if (_search.Fix_mods[i].Trim().Length > 0)
{
pFsw.WriteLine("fix_mod" + (i + 1).ToString() + "=" + _search.Fix_mods[i]);
}
}
pFsw.WriteLine();
// 可变修饰参数
pFsw.WriteLine("[modify]");
pFsw.WriteLine("Max_mod_num=" + _search.Max_mod.ToString());
pFsw.WriteLine("unexpected_mod=" + _search.UnexpectedModNum.ToString());
pFsw.WriteLine("Max_mod_mass=" + _search.MaxModMass.ToString());
pFsw.WriteLine("Modify_num=" + _search.Var_mods.Count.ToString());
for (int i = 0; i < _search.Var_mods.Count; i++)
{
if (_search.Var_mods[i].Trim().Length > 0)
{
pFsw.WriteLine("var_mod" + (i + 1).ToString() + "=" + _search.Var_mods[i]);
}
}
pFsw.WriteLine();
pFsw.WriteLine("[filter]");
pFsw.WriteLine("threshold=" + (_search.Filter.Fdr_value / 100).ToString());
pFsw.WriteLine("separate_filtering=" + (_search.Filter.SeparateFiltering ? "1" : "0"));
pFsw.WriteLine();
pFsw.WriteLine("[file]");
pFsw.WriteLine("Database=" + _search.Db.Db_path);
pFsw.WriteLine("pParseTD_cfg=" + _task.Path + "param\\pParseTD.cfg");
if (_quantitation.Quantitation_type != (int)Quant_Type.Label_None)
{
pFsw.WriteLine("pQuant_cfg=" + _task.Path + "param\\pQuant.cfg");
}
else
{
pFsw.WriteLine("pQuant_cfg=");
}
pFsw.WriteLine("outputpath=" + _task.Path);
pFsw.WriteLine();
#region Quant
pFsw.WriteLine("[quantify]");
if (_quantitation.Quantitation_type == (int)Quant_Type.Label_None)
{
pFsw.WriteLine("quant=1|none");
}
else // quantify based on MS: Quant_Type.Labeling_15N || Quant_Type.Labeling_Dimethyl || Quant_Type.Labeling_SILAC || others
{
string labels = "quant=" + _quantitation.Labeling.Multiplicity.ToString(); //Multiplicity
if (_quantitation.Labeling.Multiplicity == 1) // 1种标记
{
if (_quantitation.Labeling.Medium_label.Count == 0)
{
labels += "|none";
}
else
{
labels += "|" + _quantitation.Labeling.Medium_label[0];
}
}
else if (_quantitation.Labeling.Multiplicity == 2) // 2种标记
{
if (_quantitation.Labeling.Light_label.Count == 0) //light label
{
labels += "|none";
}
else
{
labels += "|" + _quantitation.Labeling.Light_label[0];
}
if (_quantitation.Labeling.Heavy_label.Count == 0) //heavy label
{
labels += "|none";
}
else
{
labels += "|" + _quantitation.Labeling.Heavy_label[0];
}
}
else if (_quantitation.Labeling.Multiplicity == 3) // 3种标记
{
if (_quantitation.Labeling.Light_label.Count == 0) //light label
{
labels += "|none";
}
else
{
labels += "|" + _quantitation.Labeling.Light_label[0];
}
if (_quantitation.Labeling.Medium_label.Count == 0) //medium label
{
labels += "|none";
}
else
{
labels += "|" + _quantitation.Labeling.Medium_label[0];
}
if (_quantitation.Labeling.Heavy_label.Count == 0) //heavy label
{
labels += "|none";
}
else
{
labels += "|" + _quantitation.Labeling.Heavy_label[0];
}
}
pFsw.WriteLine(labels);
}
pFsw.WriteLine();
#endregion
pFsw.WriteLine("[system]");
pFsw.WriteLine("log=LOG_INFO");
pFsw.Close();
pFfst.Close();
}
catch (Exception exe)
{
throw new Exception(exe.Message);
}
}
//read from pQuant.qnt
//wrm20150821:将来代码重构时可考虑在读参数文件时，先获取‘=’前和‘=’后的部分，再给参数赋值
void pQuant_Inter.readpQuant_qnt(string task_path, ref _Task _task)
{
string strLine = "";
try
{
FileStream fst = new FileStream(task_path + "\\param\\pQuant.cfg", FileMode.Open);
StreamReader sr = new StreamReader(fst, Encoding.Default);
strLine = sr.ReadLine();
#region
Quantitation _quant = _task.T_Quantify;
string[] labels = { "" };;
while (strLine != null)
{
strLine = strLine.Trim();
if (strLine.Length > 0 && strLine.Contains("="))
{
if (strLine.Length > ("NUMBER_MAX_PSM_PER_BLOCK").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("NUMBER_MAX_PSM_PER_BLOCK"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_advanced.Number_max_psm_per_block = int.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("TYPE_START").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("TYPE_START"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_advanced.Type_start = int.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("EXTENSION_TEXT_MS1").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("EXTENSION_TEXT_MS1"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_advanced.Extension_text_ms1 = strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1);
}
//else if (strLine.Length > ("LL_INFO_LABEL").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("LL_INFO_LABEL"))
//{
// int tmp=strLine.LastIndexOf("=");
// string qt = strLine.Substring(tmp + 1,strLine.LastIndexOf(";")-tmp-1);
// labels = qt.Split('|');
// lb = int.Parse(labels[0]);
//}
else if (strLine.Length > ("LL_ELEMENT_ENRICHMENT_CALIBRATION").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("LL_ELEMENT_ENRICHMENT_CALIBRATION"))
{
int tmp = strLine.LastIndexOf("=");
string lfec = strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1);
_quant.Quant_advanced.Ll_element_enrichment_calibration = (int)LL_ELEMENT_ENRICHMENT_CALIBRATION.None;
if (lfec.ToLower() == "15n")
{
_quant.Quant_advanced.Ll_element_enrichment_calibration = (int)LL_ELEMENT_ENRICHMENT_CALIBRATION.N15;
}
else if (lfec.ToLower() == "13c")
{
_quant.Quant_advanced.Ll_element_enrichment_calibration = (int)LL_ELEMENT_ENRICHMENT_CALIBRATION.C13;
}
//bool is15N = false;
//if (lb == 2 && labels.Length == 3 && (labels[1].Equals(ConfigHelper.N15_label) || labels[2].Equals(ConfigHelper.N15_label)))
//{
// is15N = true;
//}
//if (is15N && (flag == 1 || flag == 2))
//{
// _quant.Quantitation_type = (int)Quant_Type.Labeling_15N;
//}
}
#region Todo LabelFree
else if (strLine.Length > ("LF_INFO_SAMPLE").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("LF_INFO_SAMPLE"))
{
}
#endregion
else if (strLine.Length > ("NUMBER_SCANS_HALF_CMTG").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("NUMBER_SCANS_HALF_CMTG"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_advanced.Number_scans_half_cmtg = int.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("PPM_FOR_CALIBRATION").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("PPM_FOR_CALIBRATION"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_advanced.Ppm_for_calibration = double.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("PPM_HALF_WIN_ACCURACY_PEAK").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("PPM_HALF_WIN_ACCURACY_PEAK"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_advanced.Ppm_half_win_accuracy_peak = double.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("NUMBER_HOLE_IN_CMTG").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("NUMBER_HOLE_IN_CMTG"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_advanced.Number_hole_in_cmtg = int.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1)) - 1;
}
else if (strLine.Length > ("TYPE_SAME_START_END_BETWEEN_EVIDENCE").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("TYPE_SAME_START_END_BETWEEN_EVIDENCE"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_advanced.Type_same_start_end_between_evidence = int.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("TYPE_PEPTIDE_RATIO").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("TYPE_PEPTIDE_RATIO"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_inference.Type_peptide_ratio = int.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("TYPE_PROTEIN_RATIO_CALCULATION").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("TYPE_PROTEIN_RATIO_CALCULATION"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_inference.Type_protein_ratio_calculation = int.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("TYPE_UNIQUE_PEPTIDE_ONLY").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("TYPE_UNIQUE_PEPTIDE_ONLY"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_inference.Type_unique_peptide_only = int.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("THRESHOLD_SCORE_INTERFERENCE").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("THRESHOLD_SCORE_INTERFERENCE"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_inference.Threshold_score_interference = double.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("THRESHOLD_SCORE_INTENSITY").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("THRESHOLD_SCORE_INTENSITY"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_inference.Threshold_score_intensity = double.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
else if (strLine.Length > ("TYPE_GET_GROUP").Length && strLine.Substring(0, strLine.LastIndexOf("=")).Equals("TYPE_GET_GROUP"))
{
int tmp = strLine.LastIndexOf("=");
_quant.Quant_inference.Type_get_group = int.Parse(strLine.Substring(tmp + 1, strLine.LastIndexOf(";") - tmp - 1));
}
}
strLine = sr.ReadLine();
}
#endregion
sr.Close();
fst.Close();
}
catch (Exception exe)
{
throw new Exception("[pQuant_read] line: " + strLine + "\n" + exe.Message);
}
}
private void WritePeptides(Dictionary<string, ExperimentGroup> expgroups, string outputDirectory)
{
foreach (Peptide pep in Peptides.Values)
{
if (pep.ProteinGroups == null || pep.ProteinGroups.Count < 1) continue;
pep.ProteinGroups.Sort(ProteinGroup.CompareIncreasing);
pep.BestPG = pep.ProteinGroups[0];
}
// Loop over each experiment
foreach (ExperimentGroup exp in expgroups.Values)
{
string experimentName = exp.Name;
List<CsvFile> files = exp.CsvFiles;
StreamWriter writer = null;
if (IncludeNonFilteredResults)
{
string filename = "";
if (string.IsNullOrEmpty(experimentName))
{
filename = Path.Combine(outputDirectory, "Parsimony_peptides.csv");
}
else
{
filename = Path.Combine(outputDirectory, string.Format("{0}_parsimony_peptides.csv", experimentName));
}
Log("Writing file {0}", filename);
writer = new StreamWriter(filename);
}
string filteredfilename = "";
if (string.IsNullOrEmpty(experimentName))
{
filteredfilename = Path.Combine(outputDirectory, "Parsimony_peptides_filtered.csv");
}
else
{
filteredfilename = Path.Combine(outputDirectory, string.Format("{0}_parsimony_peptides_filtered.csv", experimentName));
}
Log("Writing file {0}", filteredfilename);
StreamWriter filteredwriter = new StreamWriter(filteredfilename);
string header = exp.Header + ",Experiment Name,# of Sharing PGs,Best PG Name";
if (IncludeNonFilteredResults)
{
writer.WriteLine(header);
}
filteredwriter.WriteLine(header);
foreach (CsvFile csvfile in files)
{
string sequenceString = "Peptide";
//string spectrumNumberString = "Spectrum number";
//string pvalueString = "P-value";
// Open up the csvfile and read it's contents, skipping the header
using (CsvReader reader = new CsvReader(new StreamReader(csvfile.FilePath), true))
{
bool pdOutput = false;
if (reader.GetFieldHeaders().Contains("XCorr"))
{
sequenceString = "Sequence";
//spectrumNumberString = "RT [min]";
//pvalueString = "PEP";
pdOutput = true;
}
int deflineIndex = reader.GetFieldIndex("Defline");
int modIndex = reader.GetFieldIndex("Mods");
int startRes = reader.GetFieldIndex("Start");
int stopRes = reader.GetFieldIndex("Stop");
Peptide pep = null;
// Read in each psm
while (reader.ReadNextRecord())
{
string seq = reader[sequenceString].ToUpper();
string leuSeq = seq.Replace('I', 'L');
string[] data = new string[reader.FieldCount];
if (Peptides.TryGetValue(leuSeq, out pep))
{
if (pep.BestPG == null || pep.BestPG.IsDecoy) continue;
foreach (ProteinGroup pg in pep.ProteinGroups)
{
exp.ProteinGroups.Add(pg);
int psms = 0;
if (pg.PsmsPerGroup.TryGetValue(exp, out psms))
{
psms++;
pg.PsmsPerGroup[exp] = psms;
}
else
{
pg.PsmsPerGroup.Add(exp, 1);
}
HashSet<Peptide> peptides = null;
if (pg.UniquePeptidesPerGroup.TryGetValue(exp, out peptides))
{
peptides.Add(pep);
}
else
{
peptides = new HashSet<Peptide>();
peptides.Add(pep);
pg.UniquePeptidesPerGroup.Add(exp, peptides);
}
}
// If performing quantitation
if (exp.UseQuant)
{
// Only use unshared Peptides
bool usePeptideInQuant = !pep.IsShared;
if (usePeptideInQuant)
{
string mod_line = reader["Mods"];
if (!string.IsNullOrEmpty(mod_line))
{
string[] mods = mod_line.Split(',');
foreach (string mod in mods)
{
string mod_name = mod.Split(':')[0];
Modification testmod = new Modification(mod_name);
if (ModificationsToIgnore.Contains(testmod))
{
usePeptideInQuant = false;
break;
}
}
}
}
if (usePeptideInQuant)
{
Quantitation quant = null;
double[] quantData = new double[4 * (int)exp.QuantPlex];
bool keepPeptide = true;
// Read in all the quant data from the csvfile
int j = 0;
for (int i = exp.TQStart; i <= exp.TQStop; i++)
{
double value = 0;
if (double.TryParse(reader[i], out value))
{
quantData[j] = value;
}
else
{
quantData[j] = 0;
}
if (IgnorePeptideWithMissingData && quantData[j] == 0)
{
keepPeptide = false;
break;
}
j++;
}
int detectedChannels = int.Parse(reader[exp.TQStop + 1]);
int totalChannels = (int) exp.QuantPlex;
bool isMissingChannel = detectedChannels != totalChannels;
if (keepPeptide)
{
//pep.SetQuantData(quantData);
// append/add the quant data to the best and only protein group
if (pep.BestPG.Quantitation.TryGetValue(exp.Name, out quant))
{
quant.AddData(pep, quantData, isMissingChannel);
}
else
{
quant = new Quantitation(exp.QuantPlex, pep, quantData, isMissingChannel);
pep.BestPG.Quantitation.Add(exp.Name, quant);
}
}
}
}
StringBuilder sb = new StringBuilder();
for (int i = 0; i < reader.FieldCount; i++)
{
data[i] = reader[i];
if (!pdOutput)
{
if (i == deflineIndex)
{
data[i] = pep.BestPG.RepresentativeProtein.Description;
}
else if (i == modIndex)
{
if (data[i].Contains(','))
data[i] = "\"" + data[i] + "\"";
}
else if (i == startRes)
{
data[i] =
pep.BestPG.RepresentativeProtein.FindStartResidue(pep.LeucineSequence)
.ToString();
}
else if (i == stopRes)
{
data[i] =
pep.BestPG.RepresentativeProtein.FindStopResidue(pep.LeucineSequence)
.ToString();
}
}
//if(data[i].Contains(','))
// data[i] = "\"" + data[i] + "\"";
sb.Append(data[i]);
sb.Append(',');
}
sb.Append(exp.Name);
sb.Append(',');
sb.Append(pep.NumberOfSharingProteinGroups);
sb.Append(',');
foreach (ProteinGroup pg2 in pep.ProteinGroups)
{
sb.Append(pg2.Name);
sb.Append('|');
}
sb.Remove(sb.Length - 1, 1);
if (IncludeNonFilteredResults)
{
writer.WriteLine(sb);
}
if (pep.BestPG.PassesFDR)
{
filteredwriter.WriteLine(sb);
}
}
else
{
throw new Exception("Read in a PSM that isn't mapped! Did an input CSV's contents change?");
}
}
}
}
if (IncludeNonFilteredResults)
writer.Close();
filteredwriter.Close();
}
}
//generate pQuant.qnt
void pQuant_Inter.pQuant_write(_Task _task)
{
try
{
Quantitation _quant = _task.T_Quantify;
pTop.classes.File _file = _task.T_File;
string filepath = _task.Path + "param\\pQuant.cfg";
FileStream qfst = new FileStream(filepath, FileMode.Create, FileAccess.Write);
StreamWriter qsw = new StreamWriter(qfst, Encoding.Default);
qsw.WriteLine("# This is a standard pQuant configure file.");
qsw.WriteLine("# Dear user,After '=' and before ';' is the content you can modify.");
qsw.WriteLine("# Please keep serious when configuring. For some of the options,you can use the default value.");
qsw.WriteLine("# For help: mail to [email protected]");
qsw.WriteLine("# Time: " + DateTime.Now.ToString());
qsw.WriteLine();
qsw.WriteLine("[INI]");
qsw.WriteLine("PATH_INI_ELEMENT=" + ConfigHelper.startup_path + "\\element.ini;");
qsw.WriteLine("PATH_INI_MODIFICATION=" + ConfigHelper.startup_path + "\\modification.ini;");
qsw.WriteLine("PATH_INI_RESIDUE=" + ConfigHelper.startup_path + "\\aa.ini;");
qsw.WriteLine();
qsw.WriteLine("[Performance]");
qsw.WriteLine("PATH_BIN=" + ConfigHelper.startup_path + ";");
qsw.WriteLine("NUMBER_MAX_PSM_PER_BLOCK=" + _quant.Quant_advanced.Number_max_psm_per_block + ";");
qsw.WriteLine("TYPE_START=" + _quant.Quant_advanced.Type_start + ";");
qsw.WriteLine();
qsw.WriteLine("[MS1]");
string ms1path = "";
for (int i = 0; i < _file.Data_file_list.Count; i++)
{
string tmp = _file.Data_file_list[i].FilePath;
ms1path += tmp.Substring(0, tmp.LastIndexOf(".")) + ".pf1|";
}
qsw.WriteLine("PATH_MS1=" + ms1path + ";");
qsw.WriteLine("EXTENSION_TEXT_MS1=" + _quant.Quant_advanced.Extension_text_ms1 + ";");
qsw.WriteLine();
qsw.WriteLine("[Identification]");
#region TODO是否有多个spectra
#endregion
string resultfile = ConfigHelper.getFileBySuffix(_task.Path, "spectra");
qsw.WriteLine("PATH_IDENTIFICATION_FILE=" + resultfile + "|;");
qsw.WriteLine("TYPE_IDENTIFICATION_FILE=2;"); //0是老pBuild;1是prolucid;2是pFind3.0
//2014.10.29 chihao：pQuant过滤阈值修改，保持与过滤时一致
qsw.WriteLine("THRESHOLD_FDR=" + (_task.T_Identify.Filter.Fdr_value / 100.0).ToString() + ";");
qsw.WriteLine();
qsw.WriteLine("[Quantitation]");
//迟浩：定量初始值设置为0，表示标记定量。在搜非标记数据时，也是跑标记流程（画三维图）
string type_label = "0";
if (_quant.Quantitation_type == (int)Quant_Type.Label_free)
{
type_label = "1";
}
qsw.WriteLine("TYPE_LABEL=" + type_label + ";");
string labelInfo = "";
#region 代码冗余
//迟浩：这一段代码写得不好，建议一起过一遍功能然后优化实现
if (_quant.Quantitation_type == (int)Quant_Type.Label_None)
{
labelInfo = "1|none";
}
else if (_quant.Quantitation_type == (int)Quant_Type.Labeling) //multiplicity=2
{
int label_num = _quant.Labeling.Multiplicity;
labelInfo = label_num.ToString();
if (label_num == 1)
{
labelInfo += "|";
if (_quant.Labeling.Medium_label.Count == 0)
{
labelInfo += "none";
}
else
{
labelInfo += _quant.Labeling.Medium_label[0];
}
}
else if (label_num == 2)
{
if (_quant.Labeling.Light_label.Count == 0 && _quant.Labeling.Heavy_label.Count == 0)
{
labelInfo = "1|none";
}
else
{
labelInfo += "|";
if (_quant.Labeling.Light_label.Count == 0)
{
labelInfo += "none";
}
else
{
labelInfo += _quant.Labeling.Light_label[0];
}
labelInfo += "|";
if (_quant.Labeling.Heavy_label.Count == 0)
{
labelInfo += "none";
}
else
{
labelInfo += _quant.Labeling.Heavy_label[0];
}
}
}
else if (label_num == 3)
{
labelInfo += "|";
if (_quant.Labeling.Light_label.Count == 0)
{
labelInfo += "none";
}
else
{
labelInfo += _quant.Labeling.Light_label[0];
}
labelInfo += "|";
if (_quant.Labeling.Medium_label.Count == 0)
{
labelInfo += "none";
}
else
{
labelInfo += _quant.Labeling.Medium_label[0];
}
labelInfo += "|";
if (_quant.Labeling.Heavy_label.Count == 0)
{
labelInfo += "none";
}
else
{
labelInfo += _quant.Labeling.Heavy_label[0];
}
}
}
qsw.WriteLine("LL_INFO_LABEL=" + labelInfo + ";");
#endregion
string lfec = "none";
if (_quant.Quant_advanced.Ll_element_enrichment_calibration == (int)LL_ELEMENT_ENRICHMENT_CALIBRATION.N15)
{
lfec = "15N";
}
else if (_quant.Quant_advanced.Ll_element_enrichment_calibration == (int)LL_ELEMENT_ENRICHMENT_CALIBRATION.C13)
{
lfec = "13C";
}
qsw.WriteLine("LL_ELEMENT_ENRICHMENT_CALIBRATION=" + lfec + ";");
#region Todo LabelFree
//Label Free
#endregion
qsw.WriteLine("LF_INFO_SAMPLE=; //Label Free暂不考虑");
qsw.WriteLine();
qsw.WriteLine("[Evidence]");
qsw.WriteLine("NUMBER_SCANS_HALF_CMTG=" + _quant.Quant_advanced.Number_scans_half_cmtg + ";");
qsw.WriteLine("PPM_FOR_CALIBRATION=" + _quant.Quant_advanced.Ppm_for_calibration + ";");
qsw.WriteLine("PPM_HALF_WIN_ACCURACY_PEAK=" + _quant.Quant_advanced.Ppm_half_win_accuracy_peak + ";");
qsw.WriteLine("NUMBER_HOLE_IN_CMTG=" + (_quant.Quant_advanced.Number_hole_in_cmtg + 1).ToString() + ";");
qsw.WriteLine("TYPE_SAME_START_END_BETWEEN_EVIDENCE=" + _quant.Quant_advanced.Type_same_start_end_between_evidence + ";");
qsw.WriteLine();
qsw.WriteLine("[Inference]");
qsw.WriteLine("TYPE_PEPTIDE_RATIO=" + _quant.Quant_inference.Type_peptide_ratio.ToString() + ";");
qsw.WriteLine("TYPE_PROTEIN_RATIO_CALCULATION=" + _quant.Quant_inference.Type_protein_ratio_calculation + ";");
qsw.WriteLine("TYPE_UNIQUE_PEPTIDE_ONLY=" + _quant.Quant_inference.Type_unique_peptide_only + ";");
qsw.WriteLine("THRESHOLD_SCORE_INTERFERENCE=" + _quant.Quant_inference.Threshold_score_interference + ";");
qsw.WriteLine("THRESHOLD_SCORE_INTENSITY=" + _quant.Quant_inference.Threshold_score_intensity + ";");
qsw.WriteLine("TYPE_GET_GROUP=" + _quant.Quant_inference.Type_get_group + ";");
qsw.WriteLine("PATH_FASTA=" + _task.T_Identify.Db.Db_path + ";");
qsw.WriteLine();
qsw.WriteLine("[Export]");
qsw.WriteLine("DIR_EXPORT=" + _task.Path + ";"); //+ "result\\;"
qsw.WriteLine("FLAG_CREATE_NEW_FOLDER=0;"); //0表示直接使用dir_export的导出目录
qsw.Close();
qfst.Close();
}
catch (Exception exe)
{
throw new Exception(exe.Message);
}
}
