public static List <string> GeneratePeptides(List <IProtein> proteins)
{
// peptides
List <Proteases> proteases = new List <Proteases>();
foreach (string enzyme in SearchingParameters.Access.DigestionEnzyme)
{
switch (enzyme)
{
case "Chymotrypsin":
proteases.Add(Proteases.Chymotrypsin);
break;
case "GluC":
proteases.Add(Proteases.GluC);
break;
case "Pepsin":
proteases.Add(Proteases.Pepsin);
break;
case "Trypsin":
proteases.Add(Proteases.Trypsin);
break;
}
}
HashSet <string> peptides = new HashSet <string>();
ProteinDigest proteinDigest = new ProteinDigest(
SearchingParameters.Access.MissCleavage,
SearchingParameters.Access.MiniPeptideLength, proteases[0]);
foreach (IProtein protein in proteins)
{
peptides.UnionWith(proteinDigest.Sequences(protein.Sequence(),
ProteinPTM.ContainsNGlycanSite));
}
for (int i = 1; i < proteases.Count; i++)
{
proteinDigest.SetProtease(proteases[i]);
List <string> peptidesList = peptides.ToList();
foreach (string seq in peptidesList)
{
peptides.UnionWith(proteinDigest.Sequences(seq,
ProteinPTM.ContainsNGlycanSite));
}
}
return(ProteinModification.DynamicModification(
peptides, ProteinPTM.ContainsNGlycanSite,
SearchingParameters.Access.Oxidiatoin,
SearchingParameters.Access.Deamidation).ToList());
}
public void test2()
{
string fasta = @"C:\Users\Rui Zhang\Downloads\haptoglobin.fasta";
// peptides
IProteinReader proteinReader = new FastaReader();
List <IProtein> proteins = proteinReader.Read(fasta);
List <Proteases> proteases = new List <Proteases>()
{
Proteases.Trypsin, Proteases.GluC
};
HashSet <string> peptides = new HashSet <string>();
ProteinDigest proteinDigest = new ProteinDigest(2, 5, proteases[0]);
foreach (IProtein protein in proteins)
{
peptides.UnionWith(proteinDigest.Sequences(protein.Sequence(),
ProteinPTM.ContainsNGlycanSite));
}
for (int i = 1; i < proteases.Count; i++)
{
proteinDigest.SetProtease(proteases[i]);
List <string> peptidesList = peptides.ToList();
foreach (string seq in peptidesList)
{
peptides.UnionWith(proteinDigest.Sequences(seq,
ProteinPTM.ContainsNGlycanSite));
}
}
HashSet <string> peptideModifieds = ProteinModification.DynamicModification(
peptides, ProteinPTM.ContainsNGlycanSite);
foreach (var s in peptideModifieds)
{
Console.WriteLine(s);
}
Console.WriteLine(peptides.Count);
Console.WriteLine(peptideModifieds.Count);
}
public static void ReportResults(
string path,
List <SearchResult> results,
Dictionary <string, IGlycan> glycans_map)
{
List <SearchResult> res = new List <SearchResult>();
HashSet <string> seen = new HashSet <string>();
foreach (var it in results)
{
string glycan = glycans_map[it.Glycan()].Name();
string key = it.Scan().ToString() + "|" + it.ModifySite().ToString() + "|" +
it.Sequence() + "|" + glycan;
if (!seen.Contains(key))
{
seen.Add(key);
SearchResult r = it;
r.set_glycan(glycan);
res.Add(r);
}
}
using (FileStream ostrm = new FileStream(path, FileMode.OpenOrCreate, FileAccess.Write))
{
using (StreamWriter writer = new StreamWriter(ostrm))
{
writer.WriteLine("scan,peptide,glycan,site,score");
foreach (SearchResult r in res)
{
writer.WriteLine(r.Scan().ToString() + ", " +
ProteinModification.Interpret(r.Sequence()) + ","
+ r.Glycan() + "," + r.ModifySite().ToString() + "," + r.Score().ToString());
writer.Flush();
}
}
}
}
