public void TestAddDigestFeatures()
{
Sequence seq = new Sequence("Test", "AAANESAARBBBNPSBBKFFFNITFFRGGGNDTGGR");
Digest digest = new Digest();
digest.DigestProtease = ProteaseManager.CreateProtease("Trypsin_TestAddDigestFeatures", true, "RK", "P");
digest.ProteinSequence = seq;
digest.MaxMissedCleavages = 0;
digest.AddDigestFeatures();
List<DigestPeptideInfo> peptides = (List<DigestPeptideInfo>)seq.Annotation[Digest.PEPTIDE_FEATURE_TYPE];
Assert.AreEqual(4, peptides.Count);
digest.MaxMissedCleavages = 1;
digest.AddDigestFeatures();
List<DigestPeptideInfo> missedPeptides = (List<DigestPeptideInfo>)seq.Annotation[Digest.PEPTIDE_FEATURE_TYPE];
Assert.AreEqual(7, missedPeptides.Count);
IRangeLocationFilter nglycanFilter = new NGlycanFilter();
digest.MaxMissedCleavages = 0;
digest.Filter = nglycanFilter;
digest.AddDigestFeatures();
List<DigestPeptideInfo> nglycanPeptides = (List<DigestPeptideInfo>)seq.Annotation[Digest.PEPTIDE_FEATURE_TYPE];
Assert.AreEqual(2, nglycanPeptides.Count);
Assert.AreEqual("AAANESAAR", nglycanPeptides[0].PeptideSeq);
Assert.AreEqual("FFFNITFFR", nglycanPeptides[1].PeptideSeq);
}
public void TestNGlycanFilter()
{
NGlycanFilter filter = new NGlycanFilter();
filter.SetSequence(new Seq.Sequence("Test", "AAANESAAR"));
Assert.IsTrue(filter.Accept(new RangeLocation(1, 9)));
filter.SetSequence(new Seq.Sequence("Test", "BBBNPSBBK"));
Assert.IsFalse(filter.Accept(new RangeLocation(1, 9)));
filter.SetSequence(new Seq.Sequence("Test", "FFFNITFFR"));
Assert.IsTrue(filter.Accept(new RangeLocation(1, 9)));
filter.SetSequence(new Seq.Sequence("Test", "GGGNDTGGR"));
Assert.IsFalse(filter.Accept(new RangeLocation(1, 9)));
}
public override IEnumerable <string> Process(string filename)
{
FastaFormat ff = new FastaFormat();
Digest digest = new Digest();
digest.DigestProtease = ProteaseManager.FindOrCreateProtease("Trypsin", true, "RK", "P");
digest.MaxMissedCleavages = 1;
NGlycanFilter filter = new NGlycanFilter();
digest.Filter = filter;
string resultFile = filename + ".nglycan";
Dictionary <string, NGlycanValue> peptideProteinMap = new Dictionary <string, NGlycanValue>();
using (StreamReader sr = new StreamReader(filename))
{
Sequence seq;
while ((seq = ff.ReadSequence(sr)) != null)
{
digest.ProteinSequence = seq;
digest.AddDigestFeatures();
if (seq.Annotation.ContainsKey(Digest.PEPTIDE_FEATURE_TYPE))
{
bool[] isGlycans = filter.IsNglycan;
List <DigestPeptideInfo> nglycanPeptides = (List <DigestPeptideInfo>)seq.Annotation[Digest.PEPTIDE_FEATURE_TYPE];
foreach (DigestPeptideInfo dpi in nglycanPeptides)
{
if (!peptideProteinMap.ContainsKey(dpi.PeptideSeq))
{
StringBuilder sb = new StringBuilder();
for (int i = 0; i < dpi.PeptideSeq.Length; i++)
{
if (isGlycans[dpi.PeptideLoc.Min - 1 + i])
{
sb.Append(1);
}
else
{
sb.Append(0);
}
}
NGlycanValue value = new NGlycanValue();
value.NGlycanSites = sb.ToString();
peptideProteinMap[dpi.PeptideSeq] = value;
}
peptideProteinMap[dpi.PeptideSeq].Proteins.Add(parser.GetValue(dpi.ProteinName));
}
}
}
}
List <string> peptides = new List <string>(peptideProteinMap.Keys);
peptides.Sort();
using (StreamWriter sw = new StreamWriter(resultFile))
{
foreach (string pep in peptides)
{
NGlycanValue value = peptideProteinMap[pep];
sw.Write(pep + "\t" + value.NGlycanSites + "\t");
bool bFirst = true;
foreach (string protein in value.Proteins)
{
if (bFirst)
{
bFirst = false;
sw.Write(protein);
}
else
{
sw.Write(" ! " + protein);
}
}
sw.WriteLine();
}
}
return(new[] { resultFile });
}
