public void Test()
{
PseudoSequenceBuilder builder = new PseudoSequenceBuilder("KR", false);
Sequence seq = new Sequence("TEST", "EISQVFEIALKRNLPVNFEVARESGPPHMKNFVTKVSVGEFVGEGEGKSK");
builder.Build(seq);
Assert.AreEqual("EISQVFEIALRKNLPVNFEVAERSGPPHMNKFVTVKSVGEFVGEGEGSKK", seq.SeqString);
}
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 TestConstruction()
{
Sequence seq = new Sequence("test description of test", "ABCDE");
Assert.AreEqual("test", seq.Name);
Assert.AreEqual("test description of test", seq.Reference);
Assert.AreEqual("description of test", seq.Description);
Assert.AreEqual("ABCDE", seq.SeqString);
}
public void TestGetReversedSequence()
{
var options = new ReversedDatabaseBuilderOptions()
{
DecoyKey = "REVERSED",
};
var builder = new ReversedDatabaseBuilder(options);
var seq = new Sequence("sp|Q12345 sp protein", "ABCDE");
options.DecoyType = DecoyType.Start;
Assert.AreEqual("REVERSED_sp|Q12345", builder.GetReversedSequence(1, seq).Name);
options.DecoyType = DecoyType.Middle;
Assert.AreEqual("sp|REVERSED_Q12345", builder.GetReversedSequence(1, seq).Name);
}
public void WriteSequence(StreamWriter writer, Sequence seq)
{
}
public void FillSequence(Sequence seq)
{
//matched exon fill sequence
exons.ForEach(m => m.FillSequence(seq, this.Strand));
//fill direct sequence
this.DirectExpectSequence = seq.SeqString.Substring((int)this.ExpectStart, (int)(this.ExpectEnd - this.ExpectStart + 1)).ToUpper();
if (this.Strand == '-')
{
this.DirectExpectSequence = SequenceUtils.GetReverseComplementedSequence(this.DirectExpectSequence);
}
}
public void Build(Sequence seq)
{
seq.SeqString = findReg.Replace(seq.SeqString, "$2$1");
}
public void WriteSequence(StreamWriter writer, Sequence seq)
{
WriteSequence(writer, seq.Reference, seq.SeqString);
}