public void ToString_ProducesExpectedOutput()
{
string expectedSequence = "ABC-";
var aminoAcidSequenceData = AminoAcidSequence.Parse(expectedSequence);
Assert.AreEqual(expectedSequence, aminoAcidSequenceData.ToString());
}
public void Parse_ShouldAcceptTranslationStop()
{
string expectedSequence = "ABC*";
var aminoAcidSequenceData = AminoAcidSequence.Parse(expectedSequence);
Assert.AreEqual(expectedSequence, aminoAcidSequenceData.Characters);
}
public void ToInterleavedLines_ShouldProduceExpectedOutputForNonDefaultLineLength()
{
string inputSequence = "MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSS"
+ "EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL";
IEnumerable <string> expectedOutputLines = new string[] {
">lcl|123",
"MDSKGSSQ",
"KGSRLLLL",
"LVVSNLLL",
"CQGVVSTP",
"VCPNGPGN",
"CQVSLRDL",
"FDRAVMVS",
"HYIHDLSS",
"EMFNEFDK",
"RYAQGKGF",
"ITMALNSC",
"HTSSLPTP",
"EDKEQAQQ",
"THHEVLMS",
"LILGLLRS",
"WNDPLYHL"
};
Identifier identifier = new LocalIdentifier("123");
Header header = new Header(identifier);
IActualSequence sequence = AminoAcidSequence.Parse(inputSequence);
var singleFASTAFileData = new Sequence(header, sequence);
IEnumerable <string> actualOutputLines = singleFASTAFileData.ToInterleavedLines(8);
CollectionAssert.AreEqual(expectedOutputLines.ToList(), actualOutputLines.ToList());
}
public void Parse_ShouldAcceptGaps()
{
string expectedSequence = "ABC-";
var aminoAcidSequenceData = AminoAcidSequence.Parse(expectedSequence);
Assert.AreEqual(expectedSequence, aminoAcidSequenceData.Characters);
}
public void ToLines_RejectsLineLengthOfZero()
{
string sequence = "ABCDEF";
var aminoAcidSequenceData = AminoAcidSequence.Parse(sequence);
_ = aminoAcidSequenceData.ToLines(0);
}
public void ToLines_RejectsNegativeLineLength()
{
string sequence = "ABCDEF";
var aminoAcidSequenceData = AminoAcidSequence.Parse(sequence);
_ = aminoAcidSequenceData.ToLines(-1);
}
private static void ValidateSequences(AminoAcidSequence seqresSequence, AminoAcidSequence atomSequence)
{
var seqresQueue = new Queue <AminoAcidSequenceItem>(seqresSequence);
var atomSequenceQueue = new Queue <AminoAcidSequenceItem>(atomSequence);
while (seqresQueue.Any() && atomSequenceQueue.Any())
{
}
}
public void ToMultilineString_ProducesExpectedOutput()
{
string sequence = "ABCDEF";
string expectedLines = $"ABCD{Environment.NewLine}EF";
var aminoAcidSequenceData = AminoAcidSequence.Parse(sequence);
string actualLines = aminoAcidSequenceData.ToMultilineString(4);
Assert.AreEqual(expectedLines, actualLines);
}
public void ToLines_ProducesExpectedOutput()
{
string sequence = "ABCDEF";
var expectedLines = new string[] { "ABCD", "EF" };
var aminoAcidSequenceData = AminoAcidSequence.Parse(sequence);
IEnumerable <string> actualLines = aminoAcidSequenceData.ToLines(4);
Assert.IsTrue(actualLines.SequenceEqual(expectedLines));
}
public void ToInterleavedLines_ShouldRejectLineLengthOfZero()
{
string inputSequence = "MDSKGSSQKGSRLLLLLVVSNLLLCQGVVSTPVCPNGPGNCQVSLRDLFDRAVMVSHYIHDLSS"
+ "EMFNEFDKRYAQGKGFITMALNSCHTSSLPTPEDKEQAQQTHHEVLMSLILGLLRSWNDPLYHL";
Identifier identifier = new LocalIdentifier("123");
Header header = new Header(identifier);
IActualSequence sequence = AminoAcidSequence.Parse(inputSequence);
var singleFASTAFileData = new Sequence(header, sequence);
_ = singleFASTAFileData.ToInterleavedLines(0).ToList();
}
public static Peptide PeptideFromSequence(AminoAcidSequence aminoAcidNameSequence, PeptideBuilderOptions options = null)
{
if (options == null)
{
options = new PeptideBuilderOptions();
}
if (options.BuildMolecule)
{
var aminoAcidReferences = aminoAcidNameSequence
.Select(sequenceItem => AminoAcidLibrary.Get(sequenceItem.AminoAcidName, sequenceItem.ResidueNumber));
return(PeptideFromAminoAcids(aminoAcidReferences));
}
else
{
var aminoAcidReferences = aminoAcidNameSequence
.Select((aa, idx) => new AminoAcidReference(aa.AminoAcidName, aa.ResidueNumber, null, new List <uint>(), 0, 0))
.ToList();
return(new Peptide(new MoleculeReference(new Molecule()), aminoAcidReferences));
}
}
private void SetModifications(PhosphoRSInput input)
{
_modifications = input.Modifications;
_aminoAcidModifications = _modifications.Select(
modification => new AminoAcidModification(
modification.Symbol,
modification.Name,
modification.Abbreviation,
modification.NeutralLossAbbreviation,
modification.MassDelta,
modification.NeutralLoss,
AminoAcidSequence.ParseAASequence(modification.TargetAminoAcids)
)
).ToList();
_phosphoModification = _aminoAcidModifications
.Where(modification => modification.ID == _options.PhosphorylationSymbol)
.First();
_phosphoTargetAminoAcids = _phosphoModification.TargetAminoAcids
.Select(a => a.OneLetterCode)
.ToArray();
}
public void Parse_ShouldRejectInvalidCharacterAtEnd()
{
_ = AminoAcidSequence.Parse("ABC2");
}
private void SetSpectra(PhosphoRSInput input)
{
_spectra = input.Spectra;
_spectrumMap = new Dictionary <int, Spectrum>();
_peptideMap = new Dictionary <int, Peptide>();
_phosphoSiteMap = new Dictionary <int, List <int> >();
_items = new List <Tuple <PeptideSpectrumMatch, List <Tuple <int, List <int> > > > >();
var count = 0;
foreach (var spectrum in input.Spectra)
{
var rank = 0;
foreach (var peptide in spectrum.IdentifiedPhosphorPeptides)
{
if (_options.MaxHitRank > 0 && rank >= _options.MaxHitRank)
{
break;
}
rank += 1;
var isoformMap = new List <Tuple <int, List <int> > >();
var aas = AminoAcidSequence.Create(
peptide.ID,
peptide.Sequence,
_aminoAcidModifications,
peptide.Modification
);
var psm = new PeptideSpectrumMatch(
peptide.ID,
spectrum.ActivationType,
spectrum.PrecursorCharge,
1,
spectrum.Peaks.ToArray(),
aas
);
var phosphoCount = peptide.Modification
.Skip(2).SkipLast(2)
.Where(c => c == _options.PhosphorylationSymbol)
.Count();
if (phosphoCount == 0)
{
continue;
}
var targetSites = peptide.Sequence
.Select((c, i) => _phosphoTargetAminoAcids.Contains(c) ? i : -1)
.Where(i => i >= 0)
.ToList();
targetSites.Combinations(phosphoCount).Take(_options.MaxIsoformCount).ForEach(sites =>
{
var list = sites.ToList();
isoformMap.Add(
new Tuple <int, List <int> >(
count,
list
)
);
_spectrumMap.Add(count, spectrum);
_peptideMap.Add(count, peptide);
_phosphoSiteMap.Add(count, list);
count += 1;
});
_items.Add(Tuple.Create <PeptideSpectrumMatch, List <Tuple <int, List <int> > > >(
psm,
isoformMap
));
}
}
}
public void Parse_ShouldRejectNullString()
{
_ = AminoAcidSequence.Parse(null);
}
public void Parse_ShouldRejectInvalidCharacterAtStart()
{
_ = AminoAcidSequence.Parse("2ABC");
}
public void Parse_ShouldConvertLowercaseSequenceToUppercase()
{
var aminoAcidSequenceData = AminoAcidSequence.Parse("abc");
Assert.AreEqual("ABC", aminoAcidSequenceData.Characters);
}
public void Parse_ShouldConvertMultilineSequenceToSingleLine()
{
var aminoAcidSequenceData = AminoAcidSequence.Parse("ABC\nDEF");
Assert.AreEqual("ABCDEF", aminoAcidSequenceData.Characters);
}