protected override void ParseSpecial(SequestParam result, List <String> contents, Dictionary <string, Pair <string, string> > parameters) { result.Normalize_Score = int.Parse(parameters["normalize_xcorr"].First); ParseEnzyme(result, contents, parameters); }
public void TestAminoacidToModification() { Assert.AreEqual(SequestStaticModification.add_G_Glycine, SequestParam.AminoacidToModification('G')); Assert.AreEqual(SequestStaticModification.add_A_Alanine, SequestParam.AminoacidToModification('A')); Assert.AreEqual(SequestStaticModification.add_S_Serine, SequestParam.AminoacidToModification('S')); Assert.AreEqual(SequestStaticModification.add_P_Proline, SequestParam.AminoacidToModification('P')); Assert.AreEqual(SequestStaticModification.add_V_Valine, SequestParam.AminoacidToModification('V')); Assert.AreEqual(SequestStaticModification.add_T_Threonine, SequestParam.AminoacidToModification('T')); Assert.AreEqual(SequestStaticModification.add_C_Cysteine, SequestParam.AminoacidToModification('C')); Assert.AreEqual(SequestStaticModification.add_L_Leucine, SequestParam.AminoacidToModification('L')); Assert.AreEqual(SequestStaticModification.add_I_Isoleucine, SequestParam.AminoacidToModification('I')); Assert.AreEqual(SequestStaticModification.add_X_LorI, SequestParam.AminoacidToModification('X')); Assert.AreEqual(SequestStaticModification.add_N_Asparagine, SequestParam.AminoacidToModification('N')); Assert.AreEqual(SequestStaticModification.add_O_Ornithine, SequestParam.AminoacidToModification('O')); Assert.AreEqual(SequestStaticModification.add_B_avg_NandD, SequestParam.AminoacidToModification('B')); Assert.AreEqual(SequestStaticModification.add_D_Aspartic_Acid, SequestParam.AminoacidToModification('D')); Assert.AreEqual(SequestStaticModification.add_Q_Glutamine, SequestParam.AminoacidToModification('Q')); Assert.AreEqual(SequestStaticModification.add_K_Lysine, SequestParam.AminoacidToModification('K')); Assert.AreEqual(SequestStaticModification.add_Z_avg_QandE, SequestParam.AminoacidToModification('Z')); Assert.AreEqual(SequestStaticModification.add_E_Glutamic_Acid, SequestParam.AminoacidToModification('E')); Assert.AreEqual(SequestStaticModification.add_M_Methionine, SequestParam.AminoacidToModification('M')); Assert.AreEqual(SequestStaticModification.add_H_Histidine, SequestParam.AminoacidToModification('H')); Assert.AreEqual(SequestStaticModification.add_F_Phenylalanine, SequestParam.AminoacidToModification('F')); Assert.AreEqual(SequestStaticModification.add_R_Arginine, SequestParam.AminoacidToModification('R')); Assert.AreEqual(SequestStaticModification.add_Y_Tyrosine, SequestParam.AminoacidToModification('Y')); Assert.AreEqual(SequestStaticModification.add_W_Tryptophan, SequestParam.AminoacidToModification('W')); }
private void ParseEnzyme(SequestParam result, List <string> contents, Dictionary <string, Pair <string, string> > parameters) { bool bFound = false; foreach (String line in contents) { if (line.StartsWith("enzyme_info")) { String[] parts = line.Split('='); String[] parts2 = Regex.Split(parts[1].Trim(), @"\s+"); result.Protease = new Protease(parts2[0], parts2[2].Equals("1"), parts2[3].Equals("-") ? "" : parts2[3], parts2[4].Equals("-") ? "" : parts2[4]); bFound = true; break; } } if (!bFound) { throw new Exception("Cannot find enzyme information, are you sure it was generated from Bioworks 3.2 or upper?"); } }
private void ParseEnzyme(SequestParam result, List <string> contents, Dictionary <string, Pair <string, string> > parameters) { bool bFound = false; int enzymeNumber = 0; String enzymeLine = enzymeNumber + "."; foreach (String line in contents) { if (line.StartsWith("enzyme_number")) { String[] parts = line.Split('='); enzymeNumber = int.Parse(parts[1].Trim()); enzymeLine = enzymeNumber + "."; } else if (line.StartsWith(enzymeLine)) { String[] parts = Regex.Split(line, @"\s+"); result.Protease = new Protease(parts[1], parts[2].Equals("1"), parts[3].Equals("-") ? "" : parts[3], parts[4].Equals("-") ? "" : parts[4]); bFound = true; break; } } if (!bFound) { throw new Exception("Cannot find enzyme information, are you sure it was generated from Bioworks 3.1 or lower?"); } }
public void TestModificationToAminoacid() { Assert.AreEqual(' ', SequestParam.ModificationToAminoacid(SequestStaticModification.add_Cterm_peptide)); Assert.AreEqual(' ', SequestParam.ModificationToAminoacid(SequestStaticModification.add_Cterm_protein)); Assert.AreEqual(' ', SequestParam.ModificationToAminoacid(SequestStaticModification.add_Nterm_peptide)); Assert.AreEqual(' ', SequestParam.ModificationToAminoacid(SequestStaticModification.add_Nterm_protein)); Assert.AreEqual('G', SequestParam.ModificationToAminoacid(SequestStaticModification.add_G_Glycine)); Assert.AreEqual('A', SequestParam.ModificationToAminoacid(SequestStaticModification.add_A_Alanine)); Assert.AreEqual('S', SequestParam.ModificationToAminoacid(SequestStaticModification.add_S_Serine)); Assert.AreEqual('P', SequestParam.ModificationToAminoacid(SequestStaticModification.add_P_Proline)); Assert.AreEqual('V', SequestParam.ModificationToAminoacid(SequestStaticModification.add_V_Valine)); Assert.AreEqual('T', SequestParam.ModificationToAminoacid(SequestStaticModification.add_T_Threonine)); Assert.AreEqual('C', SequestParam.ModificationToAminoacid(SequestStaticModification.add_C_Cysteine)); Assert.AreEqual('L', SequestParam.ModificationToAminoacid(SequestStaticModification.add_L_Leucine)); Assert.AreEqual('I', SequestParam.ModificationToAminoacid(SequestStaticModification.add_I_Isoleucine)); Assert.AreEqual('X', SequestParam.ModificationToAminoacid(SequestStaticModification.add_X_LorI)); Assert.AreEqual('N', SequestParam.ModificationToAminoacid(SequestStaticModification.add_N_Asparagine)); Assert.AreEqual('O', SequestParam.ModificationToAminoacid(SequestStaticModification.add_O_Ornithine)); Assert.AreEqual('B', SequestParam.ModificationToAminoacid(SequestStaticModification.add_B_avg_NandD)); Assert.AreEqual('D', SequestParam.ModificationToAminoacid(SequestStaticModification.add_D_Aspartic_Acid)); Assert.AreEqual('Q', SequestParam.ModificationToAminoacid(SequestStaticModification.add_Q_Glutamine)); Assert.AreEqual('K', SequestParam.ModificationToAminoacid(SequestStaticModification.add_K_Lysine)); Assert.AreEqual('Z', SequestParam.ModificationToAminoacid(SequestStaticModification.add_Z_avg_QandE)); Assert.AreEqual('E', SequestParam.ModificationToAminoacid(SequestStaticModification.add_E_Glutamic_Acid)); Assert.AreEqual('M', SequestParam.ModificationToAminoacid(SequestStaticModification.add_M_Methionine)); Assert.AreEqual('H', SequestParam.ModificationToAminoacid(SequestStaticModification.add_H_Histidine)); Assert.AreEqual('F', SequestParam.ModificationToAminoacid(SequestStaticModification.add_F_Phenylalanine)); Assert.AreEqual('R', SequestParam.ModificationToAminoacid(SequestStaticModification.add_R_Arginine)); Assert.AreEqual('Y', SequestParam.ModificationToAminoacid(SequestStaticModification.add_Y_Tyrosine)); Assert.AreEqual('W', SequestParam.ModificationToAminoacid(SequestStaticModification.add_W_Tryptophan)); }
public void TestNameToModification() { Assert.AreEqual(SequestStaticModification.add_Cterm_peptide, SequestParam.NameToModification("add_Cterm_peptide")); Assert.AreEqual(SequestStaticModification.add_Cterm_protein, SequestParam.NameToModification("add_Cterm_protein")); Assert.AreEqual(SequestStaticModification.add_Nterm_peptide, SequestParam.NameToModification("add_Nterm_peptide")); Assert.AreEqual(SequestStaticModification.add_Nterm_protein, SequestParam.NameToModification("add_Nterm_protein")); Assert.AreEqual(SequestStaticModification.add_G_Glycine, SequestParam.NameToModification("add_G_Glycine")); Assert.AreEqual(SequestStaticModification.add_A_Alanine, SequestParam.NameToModification("add_A_Alanine")); Assert.AreEqual(SequestStaticModification.add_S_Serine, SequestParam.NameToModification("add_S_Serine")); Assert.AreEqual(SequestStaticModification.add_P_Proline, SequestParam.NameToModification("add_P_Proline")); Assert.AreEqual(SequestStaticModification.add_V_Valine, SequestParam.NameToModification("add_V_Valine")); Assert.AreEqual(SequestStaticModification.add_T_Threonine, SequestParam.NameToModification("add_T_Threonine")); Assert.AreEqual(SequestStaticModification.add_C_Cysteine, SequestParam.NameToModification("add_C_Cysteine")); Assert.AreEqual(SequestStaticModification.add_L_Leucine, SequestParam.NameToModification("add_L_Leucine")); Assert.AreEqual(SequestStaticModification.add_I_Isoleucine, SequestParam.NameToModification("add_I_Isoleucine")); Assert.AreEqual(SequestStaticModification.add_X_LorI, SequestParam.NameToModification("add_X_LorI")); Assert.AreEqual(SequestStaticModification.add_N_Asparagine, SequestParam.NameToModification("add_N_Asparagine")); Assert.AreEqual(SequestStaticModification.add_O_Ornithine, SequestParam.NameToModification("add_O_Ornithine")); Assert.AreEqual(SequestStaticModification.add_B_avg_NandD, SequestParam.NameToModification("add_B_avg_NandD")); Assert.AreEqual(SequestStaticModification.add_D_Aspartic_Acid, SequestParam.NameToModification("add_D_Aspartic_Acid")); Assert.AreEqual(SequestStaticModification.add_Q_Glutamine, SequestParam.NameToModification("add_Q_Glutamine")); Assert.AreEqual(SequestStaticModification.add_K_Lysine, SequestParam.NameToModification("add_K_Lysine")); Assert.AreEqual(SequestStaticModification.add_Z_avg_QandE, SequestParam.NameToModification("add_Z_avg_QandE")); Assert.AreEqual(SequestStaticModification.add_E_Glutamic_Acid, SequestParam.NameToModification("add_E_Glutamic_Acid")); Assert.AreEqual(SequestStaticModification.add_M_Methionine, SequestParam.NameToModification("add_M_Methionine")); Assert.AreEqual(SequestStaticModification.add_H_Histidine, SequestParam.NameToModification("add_H_Histidine")); Assert.AreEqual(SequestStaticModification.add_F_Phenylalanine, SequestParam.NameToModification("add_F_Phenylalanine")); Assert.AreEqual(SequestStaticModification.add_R_Arginine, SequestParam.NameToModification("add_R_Arginine")); Assert.AreEqual(SequestStaticModification.add_Y_Tyrosine, SequestParam.NameToModification("add_Y_Tyrosine")); Assert.AreEqual(SequestStaticModification.add_W_Tryptophan, SequestParam.NameToModification("add_W_Tryptophan")); }
protected override void ParseSpecial(SequestParam result, List <string> contents, Dictionary <string, Pair <string, string> > parameters) { if (parameters.ContainsKey("normalize_Score")) { result.Normalize_Score = int.Parse(parameters["normalize_Score"].First); } else if (parameters.ContainsKey("normalize_score")) { result.Normalize_Score = int.Parse(parameters["normalize_score"].First); } ParseEnzyme(result, contents, parameters); }
public SequestParam ReadFromFile(String paramFilename) { List <String> contents = ReadSequestParamContents(paramFilename); Dictionary <string, Pair <string, string> > parameters = InitParameters(contents); var result = new SequestParam(); ParseCommon(result, contents, parameters); ParseSpecial(result, contents, parameters); return(result); }
public void TestAminoacidToModificationException() { SequestParam.AminoacidToModification(' '); }
public void TestNameToModificationException() { SequestParam.NameToModification(""); }
private void ParseCommon(SequestParam result, List <String> contents, Dictionary <string, Pair <string, string> > parameters) { result.First_database_name = parameters["first_database_name"].First; result.Peptide_mass_tolerance = MyConvert.ToDouble(parameters["peptide_mass_tolerance"].First); result.Ion_series = parameters["ion_series"].First; result.Fragment_ion_tolerance = MyConvert.ToDouble(parameters["fragment_ion_tolerance"].First); result.Num_output_lines = int.Parse(parameters["num_output_lines"].First); result.Num_results = int.Parse(parameters["num_results"].First); result.Num_description_lines = int.Parse(parameters["num_description_lines"].First); result.Show_fragment_ions = int.Parse(parameters["show_fragment_ions"].First); result.Print_duplicate_references = int.Parse(parameters["print_duplicate_references"].First); if (parameters.ContainsKey("max_num_differential_per_peptide")) { result.Max_num_differential_AA_per_mod = int.Parse(parameters["max_num_differential_per_peptide"].First); } else { result.Max_num_differential_AA_per_mod = int.Parse(parameters["max_num_differential_AA_per_mod"].First); } string diff_search_options = parameters["diff_search_options"].First; result.Diff_search_options.Clear(); Match m = Regex.Match(diff_search_options, @"([\d.-]+)\s+(\S+)"); if (m.Success) { do { double addMass = MyConvert.ToDouble(m.Groups[1].Value); if (addMass != 0.0) { result.Diff_search_options[m.Groups[2].Value] = addMass; } m = m.NextMatch(); } while (m.Success); } string term_diff_search_options = parameters["term_diff_search_options"].First; String[] parts1 = Regex.Split(term_diff_search_options, @"\s+"); result.Term_diff_search_options.First = MyConvert.ToDouble(parts1[0]); result.Term_diff_search_options.Second = MyConvert.ToDouble(parts1[1]); result.Nucleotide_reading_frame = int.Parse(parameters["nucleotide_reading_frame"].First); result.Mass_type_parent = int.Parse(parameters["mass_type_parent"].First); result.Mass_type_fragment = int.Parse(parameters["mass_type_fragment"].First); result.Remove_precursor_peak = int.Parse(parameters["remove_precursor_peak"].First); result.Ion_cutoff_percentage = MyConvert.ToDouble(parameters["ion_cutoff_percentage"].First); result.Max_num_internal_cleavage_sites = int.Parse(parameters["max_num_internal_cleavage_sites"].First); string protein_mass_filter = parameters["protein_mass_filter"].First; String[] parts2 = Regex.Split(protein_mass_filter, @"\s+"); result.Protein_mass_filter.First = MyConvert.ToDouble(parts2[0]); result.Protein_mass_filter.Second = MyConvert.ToDouble(parts2[1]); result.Match_peak_count = int.Parse(parameters["match_peak_count"].First); result.Match_peak_allowed_error = int.Parse(parameters["match_peak_allowed_error"].First); result.Match_peak_tolerance = MyConvert.ToDouble(parameters["match_peak_tolerance"].First); result.Partial_sequence = parameters["partial_sequence"].First; result.Sequence_header_filter = parameters["sequence_header_filter"].First; foreach (string ssm in Enum.GetNames(typeof(SequestStaticModification))) { if (parameters.ContainsKey(ssm)) { result.StaticModification[SequestParam.NameToModification(ssm)] = MyConvert.ToDouble(parameters[ssm].First); } } }
protected abstract void ParseSpecial(SequestParam result, List <String> contents, Dictionary <string, Pair <string, string> > parameters);