public static void TestGlycanCompositionHypothesis()
{
String testGlycanCompositionFile = @"TestData\Glycresoft glycan hypothesis.csv";
CompositionHypothesis glycanHypothesis = new CompositionHypothesis();
glycanHypothesis.ParseCompositionHypothesisCsv<GlycanComposition>(testGlycanCompositionFile);
Console.WriteLine(glycanHypothesis);
}
public static void TestGlycoPeptideHypothesis()
{
String testGlycopeptideCompositionFile = @"TestData\HA-USSR-Glycopeptide hypothesis.csv";
CompositionHypothesis glycopeptideHypothesis = new CompositionHypothesis();
glycopeptideHypothesis.ParseCompositionHypothesisCsv<GlycopeptideComposition>(testGlycopeptideCompositionFile);
Console.WriteLine(glycopeptideHypothesis);
}
public static void TestBuildGlycoPeptideHypothesis()
{
String testGlycanCompositionFile = @"TestData\Glycresoft glycan hypothesis.csv";
CompositionHypothesis glycanHypothesis = new CompositionHypothesis();
glycanHypothesis.ParseCompositionHypothesisCsv<GlycanComposition>(testGlycanCompositionFile);
String testMSDigestFile = @"TestData\KK-USSR-digest-Prospector output.xml";
MSDigestReport msdigest = MSDigestReport.Load(testMSDigestFile);
int counter = 0;
foreach (MSDigestPeptide pep in msdigest.Peptides)
{
counter += pep.NumGlycosylations;
if (counter > 30)
{
pep.NumGlycosylations = 0;
}
}
try
{
GlycopeptideCompositionHypothesisBuilder builder = new GlycopeptideCompositionHypothesisBuilder(glycanHypothesis, msdigest.Peptides);
Console.WriteLine("Building Hypothesis");
builder.BuildCompositionHypothesis();
Console.WriteLine(builder.GlycopeptideComposition);
builder.GlycopeptideComposition.WriteCompositionHypothesisCsv("TestData/TestOutputHypothesis.csv");
}
catch (OutOfMemoryException ex)
{
Console.WriteLine("\n\n\n!!!!!!!!!!!!!!!!Combinatorics exceeded memory size!", ex.Message, "\n\n\n!!!!!!!!!!!!!!!!!!!!!!!!!!");
}
}
public GlycopeptideCompositionHypothesisBuilder(CompositionHypothesis glycanCompositionHypothesis, List<MSDigestPeptide> peptides)
{
this.GlycanCompositions = glycanCompositionHypothesis;
this.Peptides = peptides;
this.GlycopeptideComposition = new CompositionHypothesis();
GlycopeptideComposition.ElementNames = GlycanCompositions.ElementNames;
GlycopeptideComposition.MoleculeNames = GlycanCompositions.MoleculeNames;
}
private DataTable BuildCompositionHypothesisDataTable(CompositionHypothesis.CompositionHypothesis hypothesis)
{
DataTable hypothesisTable = new DataTable();
hypothesisTable.Columns.Add("Molecular Weight", typeof(Double));
foreach (string element in hypothesis.ElementNames)
{
hypothesisTable.Columns.Add(element, typeof(Int32));
}
hypothesisTable.Columns.Add("Compositions", typeof(String));
foreach (string molecule in hypothesis.MoleculeNames)
{
hypothesisTable.Columns.Add(molecule, typeof(String));
}
hypothesisTable.Columns.Add("Adduct/Replacement", typeof(String));
hypothesisTable.Columns.Add("Adduct Amount", typeof(Int32));
hypothesisTable.Columns.Add("Peptide Sequence", typeof(String));
hypothesisTable.Columns.Add("Peptide Modification", typeof(String));
hypothesisTable.Columns.Add("Peptide Missed Cleavage Number", typeof(Int32));
hypothesisTable.Columns.Add("Number of Glycan Attachment to Peptide", typeof(Int32));
hypothesisTable.Columns.Add("Start AA", typeof(Int32));
hypothesisTable.Columns.Add("End AA", typeof(Int32));
hypothesisTable.Columns.Add("Protein ID", typeof(String));
foreach (GlycopeptideComposition entry in hypothesis.Compositions)
{
DataRow row = hypothesisTable.NewRow();
string glycanTuple = entry.GlycanCompositionTuple(hypothesis.MoleculeNames);
row["Molecular Weight"] = entry.MassWeight;
foreach (string element in hypothesis.ElementNames)
{
if (entry.ElementalComposition.ContainsKey(element))
{
row[element] = entry.ElementalComposition[element];
}
else
{
row[element] = 0;
}
}
row["Compositions"] = glycanTuple;
foreach (string molecule in hypothesis.MoleculeNames)
{
if (entry.MolecularComposition.ContainsKey(molecule))
{
row[molecule] = entry.MolecularComposition[molecule];
}
else
{
row[molecule] = 0;
}
}
row["Adduct/Replacement"] = entry.AdductReplaces;
row["Adduct Amount"] = entry.AdductAmount;
row["Peptide Sequence"] = entry.PeptideSequence;
row["Peptide Modification"] = entry.PeptideModification;
row["Peptide Missed Cleavage Number"] = entry.MissedCleavages;
row["Number of Glycan Attachment to Peptide"] = entry.GlycosylationCount;
row["Start AA"] = entry.StartAA;
row["End AA"] = entry.EndAA;
row["Protein ID"] = entry.ProteinID;
hypothesisTable.Rows.Add(row);
}
for (int i = 0; i < hypothesisTable.Columns.Count; i++ )
{
hypothesisTable.Columns[i].SetOrdinal(i);
}
return hypothesisTable;
}
