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);