private void Rescore(string msAlignFilePath, string outputFilePath) { var parser = new TsvFileParser(msAlignFilePath); var sequences = parser.GetData("Peptide"); var scanNums = parser.GetData("Scan(s)").Select(s => Convert.ToInt32(s)).ToArray(); var charges = parser.GetData("Charge").Select(c => Convert.ToInt32(c)).ToArray(); var rows = parser.GetRows(); var headers = parser.GetHeaders(); using (var writer = new StreamWriter(outputFilePath)) { writer.WriteLine("{0}\t{1}", string.Join("\t", headers), IcScores.GetScoreNames()); for (var i = 0; i < parser.NumData; i++) { var row = rows[i]; var seqStr = SimpleStringProcessing.GetStringBetweenDots(sequences[i]); if (seqStr == null || seqStr.Contains("(")) { continue; //TODO: currently ignore ids with modifications } var composition = AASet.GetComposition(seqStr); //var sequence = new Sequence(seqStr, AASet); //if (sequence == null) //{ // Console.WriteLine("Ignore illegal sequence: {0}", seqStr); // continue; //} var charge = charges[i]; var scanNum = scanNums[i]; var scores = _topDownScorer.GetScores(AminoAcid.ProteinNTerm, seqStr, AminoAcid.ProteinCTerm, composition, charge, scanNum); if (scores == null) { continue; } writer.WriteLine("{0}\t{1}", row, scores); } } }
private void Rescore(string icResultFilePath, string outputFilePath) { var parser = new TsvFileParser(icResultFilePath); var sequences = parser.GetData("Sequence"); var scanNums = parser.GetData("ScanNum").Select(s => Convert.ToInt32(s)).ToArray(); var charges = parser.GetData("Charge").Select(c => Convert.ToInt32(c)).ToArray(); var compositions = parser.GetData("Composition").Select(Composition.Parse).ToArray(); var modIndex = parser.GetHeaders().IndexOf("Modifications"); var rows = parser.GetRows(); var headers = parser.GetHeaders(); using (var writer = new StreamWriter(outputFilePath)) { writer.WriteLine("{0}\t{1}", string.Join("\t", headers), IcScores.GetScoreNames()); for (var i = 0; i < parser.NumData; i++) { var row = rows[i]; var seqStr = sequences[i]; var charge = charges[i]; var scanNum = scanNums[i]; var composition = compositions[i]; var scores = _topDownScorer.GetScores(AminoAcid.ProteinNTerm, seqStr, AminoAcid.ProteinCTerm, composition, charge, scanNum); var token = row.Split('\t'); for (var j = 0; j < token.Length; j++) { if (j != modIndex) { writer.Write(token[j] + "\t"); } else { writer.Write("[" + scores.Modifications + "]" + "\t"); } } writer.WriteLine(scores); } } }