private void AddProtein(string ID, string Description)
{
if (!myProteins.Exists((a) => a.ID.Equals(ID)))
{
try
{
ProteinInfo pt = new ProteinInfo();
if (ID.StartsWith("IPI"))
{
//remove the decimal at the end
ID = Regex.Replace(ID, @"\..*", "");
}
pt.ID = ID;
pt.Description = Description;
myProteins.Add(pt);
}
catch {
throw (new Exception("Failed parsing result report"));
}
}
}
/// <summary>
/// Load the Sequence to Protein mapping using the specified PHRP result file
/// </summary>
/// <param name="filePath"></param>
/// <param name="seqToProteinMap">Sequence to protein map</param>
/// <returns>True if successful, false if an error</returns>
private bool LoadSeqToProteinMapping(string filePath, IDictionary <int, List <ProteinInfo> > seqToProteinMap)
{
var headerLineParsed = false;
try
{
// Initialize the column mapping
// Using a case-insensitive comparer
var columnHeaders = new SortedDictionary <string, int>(StringComparer.OrdinalIgnoreCase)
{
{ SEQ_PROT_MAP_COLUMN_Unique_Seq_ID, 0 },
{ SEQ_PROT_MAP_COLUMN_Cleavage_State, 1 },
{ SEQ_PROT_MAP_COLUMN_Terminus_State, 2 },
{ SEQ_PROT_MAP_COLUMN_Protein_Name, 3 },
{ SEQ_PROT_MAP_COLUMN_Protein_EValue, 4 },
{ SEQ_PROT_MAP_COLUMN_Protein_Intensity, 5 }
};
// Read the data from the sequence to protein map file
using var reader = new StreamReader(new FileStream(filePath, FileMode.Open, FileAccess.Read, FileShare.ReadWrite));
while (!reader.EndOfStream)
{
var lineIn = reader.ReadLine();
var skipLine = false;
if (string.IsNullOrEmpty(lineIn))
{
continue;
}
var splitLine = lineIn.Split('\t');
if (!headerLineParsed)
{
if (string.Equals(splitLine[0], SEQ_PROT_MAP_COLUMN_Unique_Seq_ID, StringComparison.OrdinalIgnoreCase))
{
// Parse the header line to confirm the column ordering
ReaderFactory.ParseColumnHeaders(splitLine, columnHeaders);
skipLine = true;
}
headerLineParsed = true;
}
if (skipLine || splitLine.Length < 3)
{
continue;
}
if (!int.TryParse(splitLine[0], out var seqID))
{
continue;
}
var proteinName = ReaderFactory.LookupColumnValue(splitLine, SEQ_PROT_MAP_COLUMN_Protein_Name, columnHeaders, string.Empty);
if (string.IsNullOrEmpty(proteinName))
{
continue;
}
var cleavageState = (PeptideCleavageStateCalculator.PeptideCleavageState)ReaderFactory.LookupColumnValue(splitLine, SEQ_PROT_MAP_COLUMN_Cleavage_State, columnHeaders, 0);
var terminusState = (PeptideCleavageStateCalculator.PeptideTerminusState)ReaderFactory.LookupColumnValue(splitLine, SEQ_PROT_MAP_COLUMN_Terminus_State, columnHeaders, 0);
var proteinInfo = new ProteinInfo(proteinName, seqID, cleavageState, terminusState);
if (seqToProteinMap.TryGetValue(seqID, out var proteins))
{
// Sequence already exists in seqToProteinMap; add the new protein info
if (MaxProteinsPerSeqID == 0 || proteins.Count < MaxProteinsPerSeqID)
{
proteins.Add(proteinInfo);
}
}
else
{
// New Sequence ID
proteins = new List <ProteinInfo> {
proteinInfo
};
seqToProteinMap.Add(seqID, proteins);
}
}
}
catch (Exception ex)
{
throw new Exception("Exception loading Seq to Protein Mapping from " + Path.GetFileName(filePath) + ": " + ex.Message);
}
return(true);
}
public bool CreateReport(string TaskID, string FileName, string searchModule, string sc, int distinctPeptides)
{
//string strReportName = FileName.Substring(0, FileName.LastIndexOf(".")) + ".txt";
Dictionary <string, ProteinInfo> Proteins = new Dictionary <string, ProteinInfo>();
string strReportFile = WebConfigurationManager.ConnectionStrings["UploadPath"].ConnectionString + TaskID + "\\Result.txt";
if (File.Exists(strReportFile))
{
FileStream fs = File.Open(strReportFile, FileMode.Open, FileAccess.Read, FileShare.ReadWrite);
StreamReader sr = new StreamReader(fs);
string line;
while ((line = sr.ReadLine()) != null)
{
//the sample line:
//Y 349 CoPep00035959 0.686646308289647 0.345257544453165 0.686646308289647 60989
//N 369
string[] tokens = line.Split(new string[] { "|" }, StringSplitOptions.None);
if (tokens[0] == "Y")
{
string peptideID = tokens[2];
string strIPI = tokens[12];
//string strSQL = "select ref_protein_id,t1.protein_cop_id ,protein_name,organism_source,sequence_length from protein_tbl t1, pp_relation_tbl t2 where t1.protein_cop_id = t2.protein_cop_id and t2.peptide_cop_id = '{0}'";
//strSQL = string.Format(strSQL, peptideID);
//DBInterface.ConnectDB();
//DbDataReader result = DBInterface.QuerySQL(strSQL);
//if (result != null)
//{
// while (result.Read())
// {
// string strIPI = result.GetString (0);
if (Proteins.ContainsKey(strIPI))
{
ProteinInfo PI = Proteins[strIPI];
ScanPeptide spinfo = new ScanPeptide();
spinfo.ScanNO = tokens[1];
spinfo.PeptideID = peptideID;
spinfo.SimilarityScore = tokens[5];
spinfo.DetaM = double.Parse(tokens[6]);
spinfo.SpectrumSeq = tokens[7];
spinfo.PeptideSequence = tokens[8];
spinfo.ModifiedType = tokens[9];
spinfo.FinalScore = tokens[10];
spinfo.mzFile = tokens[11];
PI.AddScanPeptide(spinfo);
Proteins[strIPI] = PI;
}
else
{
string strCOPaID = strIPI;
string strProteinName = tokens[13];
string strOrganism;
if (this.lbSearchingModule.Text.ToLower().Contains("human"))
{
strOrganism = "H**o sapiens (Human)";
}
else
{
strOrganism = "Mus musculus (Mouse)";
}
int length = int.Parse(tokens[14]);
ProteinInfo PI = new ProteinInfo(strIPI, strCOPaID, strProteinName, strOrganism, length);
ScanPeptide spinfo = new ScanPeptide();
spinfo.ScanNO = tokens[1];
spinfo.PeptideID = peptideID;
spinfo.SimilarityScore = tokens[5];
spinfo.DetaM = double.Parse(tokens[6]);
spinfo.SpectrumSeq = tokens[7];
spinfo.PeptideSequence = tokens[8];
spinfo.ModifiedType = tokens[9];
spinfo.FinalScore = tokens[10];
spinfo.mzFile = tokens[11];
PI.AddScanPeptide(spinfo);
Proteins.Add(strIPI, PI);
}
// }
// result.Close();
//}
//DBInterface.CloseDB();
}
}
sr.Close();
}
//write the protein view info to report 2
XmlWriterSettings settings = new XmlWriterSettings();
settings.Indent = true;
settings.IndentChars = (" ");
//string strReportFile = Properties.Settings.Default.upload_path + searchInfo.task_id + "\\" + searchInfo.report_filename;
string XSLFile = strReportFile + ".xls";
strReportFile += ".xml";
//XSL table colums : SCAN, PeptideSequence, ModifiedType,Protein Access Numbers, Protein Name, Species, Protein_COPa_ID, Peptide_COPa_ID,Spectra_COPa_ID, MatchScore,DetaM
string ProteinLine = "{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}\t{11}\t{12}";
try
{
using (StreamWriter sw = new StreamWriter(XSLFile))
{
sw.WriteLine(string.Format(ProteinLine, "mzFile", "Scan", "PeptideSequence", "ModifiedType", "Protein Access Numbers", "Protein Name", "Species", "Protein COPaID", "Peptide COPaID", "Spectrum COPaID", "Similarity Score", "DetaM/Z", "Final Score"));
using (XmlWriter writer = XmlWriter.Create(strReportFile, settings))
{
writer.WriteStartElement("COPaReport");
writer.WriteAttributeString("TaskID", TaskID);
writer.WriteAttributeString("mzFile", FileName);
string strLibModule = searchModule;
writer.WriteAttributeString("LibModule", strLibModule);
writer.WriteAttributeString("SearchFilter", sc);
writer.WriteAttributeString("IDProteins", Proteins.Count.ToString());
foreach (KeyValuePair <string, ProteinInfo> kvp in Proteins)
{
ArrayList splists = kvp.Value.ScanPeptides;
if (IsPassFilter(splists, distinctPeptides))
{
writer.WriteStartElement("Proteins");
writer.WriteAttributeString("IPI", kvp.Key);
writer.WriteAttributeString("COPaID", kvp.Value.COPaID);
writer.WriteAttributeString("ProteinName", kvp.Value.ProteinName);
writer.WriteAttributeString("Organism", kvp.Value.Organism);
//ArrayList splists = kvp.Value.ScanPeptides;
writer.WriteAttributeString("SpectraCount", splists.Count.ToString());
writer.WriteAttributeString("NormalizCount", ((float)(splists.Count) / kvp.Value.ProteinLength).ToString());
foreach (ScanPeptide sp in splists)
{
writer.WriteStartElement("Scan-Peptide");
writer.WriteAttributeString("mzFile", sp.mzFile);
writer.WriteAttributeString("Scan", sp.ScanNO);
writer.WriteAttributeString("PeptideSequence", sp.PeptideSequence);
if (sp.ModifiedType != "")
{
writer.WriteAttributeString("ModifiedType", sp.ModifiedType);
}
writer.WriteAttributeString("Peptide", sp.PeptideID);
writer.WriteAttributeString("SimilarityScore", sp.SimilarityScore);
writer.WriteAttributeString("DetaMZ", sp.DetaM.ToString());
writer.WriteAttributeString("Spectrum", sp.SpectrumSeq);
writer.WriteAttributeString("FinalyScore", sp.FinalScore);
writer.WriteEndElement();
sw.WriteLine(ProteinLine, sp.mzFile, sp.ScanNO, sp.PeptideSequence, sp.ModifiedType, kvp.Key, kvp.Value.ProteinName, kvp.Value.Organism, kvp.Value.COPaID, sp.PeptideID, sp.SpectrumSeq, sp.SimilarityScore, sp.DetaM, sp.FinalScore);
}
writer.WriteEndElement();
}
}
writer.WriteEndElement();
writer.Flush();
sw.Close();
}
}
}
catch (Exception ex)
{
DBInterface.LogEvent(ex.ToString(), System.Diagnostics.EventLogEntryType.Error);
}
return(true);
}
public bool CreateReport(string TaskID, string FileName, string searchModule, string sc, int distinctPeptides)
{
//string strReportName = FileName.Substring(0, FileName.LastIndexOf(".")) + ".txt";
Dictionary<string, ProteinInfo> Proteins = new Dictionary<string, ProteinInfo>();
string strReportFile = WebConfigurationManager.ConnectionStrings["UploadPath"].ConnectionString + TaskID + "\\Result.txt";
if (File.Exists(strReportFile))
{
FileStream fs = File.Open(strReportFile, FileMode.Open, FileAccess.Read, FileShare.ReadWrite);
StreamReader sr = new StreamReader(fs);
string line;
while ((line = sr.ReadLine()) != null)
{
//the sample line:
//Y 349 CoPep00035959 0.686646308289647 0.345257544453165 0.686646308289647 60989
//N 369
string[] tokens = line.Split(new string[] { "|" }, StringSplitOptions.None);
if (tokens[0] == "Y")
{
string peptideID = tokens[2];
string strIPI = tokens[12];
//string strSQL = "select ref_protein_id,t1.protein_cop_id ,protein_name,organism_source,sequence_length from protein_tbl t1, pp_relation_tbl t2 where t1.protein_cop_id = t2.protein_cop_id and t2.peptide_cop_id = '{0}'";
//strSQL = string.Format(strSQL, peptideID);
//DBInterface.ConnectDB();
//DbDataReader result = DBInterface.QuerySQL(strSQL);
//if (result != null)
//{
// while (result.Read())
// {
// string strIPI = result.GetString (0);
if (Proteins.ContainsKey(strIPI))
{
ProteinInfo PI = Proteins[strIPI];
ScanPeptide spinfo = new ScanPeptide();
spinfo.ScanNO = tokens[1];
spinfo.PeptideID = peptideID;
spinfo.SimilarityScore = tokens[5];
spinfo.DetaM = double.Parse(tokens[6]);
spinfo.SpectrumSeq = tokens[7];
spinfo.PeptideSequence = tokens[8];
spinfo.ModifiedType = tokens[9];
spinfo.FinalScore = tokens[10];
spinfo.mzFile = tokens[11];
PI.AddScanPeptide(spinfo);
Proteins[strIPI] = PI;
}
else
{
string strCOPaID = strIPI;
string strProteinName = tokens[13];
string strOrganism;
if (this.lbSearchingModule.Text.ToLower().Contains("human"))
strOrganism = "H**o sapiens (Human)";
else
strOrganism = "Mus musculus (Mouse)";
int length = int.Parse(tokens[14]);
ProteinInfo PI = new ProteinInfo(strIPI, strCOPaID, strProteinName, strOrganism, length);
ScanPeptide spinfo = new ScanPeptide();
spinfo.ScanNO = tokens[1];
spinfo.PeptideID = peptideID;
spinfo.SimilarityScore = tokens[5];
spinfo.DetaM = double.Parse(tokens[6]);
spinfo.SpectrumSeq = tokens[7];
spinfo.PeptideSequence = tokens[8];
spinfo.ModifiedType = tokens[9];
spinfo.FinalScore = tokens[10];
spinfo.mzFile = tokens[11];
PI.AddScanPeptide(spinfo);
Proteins.Add(strIPI, PI);
}
// }
// result.Close();
//}
//DBInterface.CloseDB();
}
}
sr.Close();
}
//write the protein view info to report 2
XmlWriterSettings settings = new XmlWriterSettings();
settings.Indent = true;
settings.IndentChars = (" ");
//string strReportFile = Properties.Settings.Default.upload_path + searchInfo.task_id + "\\" + searchInfo.report_filename;
string XSLFile = strReportFile + ".xls";
strReportFile += ".xml";
//XSL table colums : SCAN, PeptideSequence, ModifiedType,Protein Access Numbers, Protein Name, Species, Protein_COPa_ID, Peptide_COPa_ID,Spectra_COPa_ID, MatchScore,DetaM
string ProteinLine = "{0}\t{1}\t{2}\t{3}\t{4}\t{5}\t{6}\t{7}\t{8}\t{9}\t{10}\t{11}\t{12}";
try
{
using (StreamWriter sw = new StreamWriter(XSLFile))
{
sw.WriteLine(string.Format(ProteinLine, "mzFile", "Scan", "PeptideSequence", "ModifiedType", "Protein Access Numbers", "Protein Name", "Species", "Protein COPaID", "Peptide COPaID", "Spectrum COPaID", "Similarity Score", "DetaM/Z", "Final Score"));
using (XmlWriter writer = XmlWriter.Create(strReportFile, settings))
{
writer.WriteStartElement("COPaReport");
writer.WriteAttributeString("TaskID", TaskID);
writer.WriteAttributeString("mzFile", FileName);
string strLibModule = searchModule;
writer.WriteAttributeString("LibModule", strLibModule);
writer.WriteAttributeString("SearchFilter", sc);
writer.WriteAttributeString("IDProteins", Proteins.Count.ToString());
foreach (KeyValuePair<string, ProteinInfo> kvp in Proteins)
{
ArrayList splists = kvp.Value.ScanPeptides;
if (IsPassFilter(splists, distinctPeptides))
{
writer.WriteStartElement("Proteins");
writer.WriteAttributeString("IPI", kvp.Key);
writer.WriteAttributeString("COPaID", kvp.Value.COPaID);
writer.WriteAttributeString("ProteinName", kvp.Value.ProteinName);
writer.WriteAttributeString("Organism", kvp.Value.Organism);
//ArrayList splists = kvp.Value.ScanPeptides;
writer.WriteAttributeString("SpectraCount", splists.Count.ToString());
writer.WriteAttributeString("NormalizCount", ((float)(splists.Count) / kvp.Value.ProteinLength).ToString());
foreach (ScanPeptide sp in splists)
{
writer.WriteStartElement("Scan-Peptide");
writer.WriteAttributeString("mzFile", sp.mzFile);
writer.WriteAttributeString("Scan", sp.ScanNO);
writer.WriteAttributeString("PeptideSequence", sp.PeptideSequence);
if (sp.ModifiedType != "")
{
writer.WriteAttributeString("ModifiedType", sp.ModifiedType);
}
writer.WriteAttributeString("Peptide", sp.PeptideID);
writer.WriteAttributeString("SimilarityScore", sp.SimilarityScore);
writer.WriteAttributeString("DetaMZ", sp.DetaM.ToString());
writer.WriteAttributeString("Spectrum", sp.SpectrumSeq);
writer.WriteAttributeString("FinalyScore", sp.FinalScore);
writer.WriteEndElement();
sw.WriteLine(ProteinLine, sp.mzFile, sp.ScanNO, sp.PeptideSequence, sp.ModifiedType, kvp.Key, kvp.Value.ProteinName, kvp.Value.Organism, kvp.Value.COPaID, sp.PeptideID, sp.SpectrumSeq, sp.SimilarityScore, sp.DetaM, sp.FinalScore);
}
writer.WriteEndElement();
}
}
writer.WriteEndElement();
writer.Flush();
sw.Close();
}
}
}
catch (Exception ex)
{
DBInterface.LogEvent(ex.ToString(), System.Diagnostics.EventLogEntryType.Error);
}
return true;
}
