/// <summary>
/// Convert the sequence information from the external types to the internal types
/// </summary>
/// <param name="peptide"></param>
/// <returns></returns>
public static Sequence GetIpSequence(this SimpleMZIdentMLReader.PeptideRef peptide)
{
var aminoAcidSet = new AminoAcidSet();
var sequence = new Sequence(peptide.Sequence, aminoAcidSet);
foreach (var mod in peptide.Mods)
{
var seqIndex = Math.Max(0, mod.Key - 1);
var mzidMod = mod.Value;
var modification = Modification.Get(mzidMod.Tag, mzidMod.Mass);
sequence[seqIndex] = new ModifiedAminoAcid(sequence[seqIndex], modification);
}
return(new Sequence(sequence));
}
/// <summary>
/// Read results from tsv file into group of objects from PSI_Interface
/// </summary>
/// <param name="idFilePath"></param>
/// <returns></returns>
public static SimpleMZIdentMLReader.SimpleMZIdentMLData ReadResultsFromFileToMzIdData(string idFilePath)
{
var databaseSearchResultData = ReadResultsFromFile(idFilePath);
var simpleMzIdentMLData = new SimpleMZIdentMLReader.SimpleMZIdentMLData(idFilePath);
foreach (var databaseSearchResult in databaseSearchResultData)
{
var peptide = new SimpleMZIdentMLReader.PeptideRef
{
Sequence = databaseSearchResult.Sequence
};
var identification = new SimpleMZIdentMLReader.SpectrumIdItem
{
Peptide = peptide,
Charge = databaseSearchResult.Charge,
ScanNum = databaseSearchResult.ScanNum,
SpecEv = databaseSearchResult.SpecEValue,
};
// Parse modification
var modParts = databaseSearchResult.Modifications.Split(',');
if (modParts.Length > 0)
{
foreach (var part in modParts)
{
var mod = part.Split(' ');
if (mod.Length < 2)
{
continue;
}
var modName = mod[0];
var modIndex = Convert.ToInt32(mod[1]);
var ipMod = Modification.Get(modName);
var modification = new SimpleMZIdentMLReader.Modification
{
Mass = ipMod.Mass,
Tag = modName,
};
peptide.ModsAdd(modIndex, modification);
}
}
var proteinAccessions = databaseSearchResult.ProteinName.Split(',');
foreach (var accession in proteinAccessions)
{
var dbSequence = new SimpleMZIdentMLReader.DatabaseSequence
{
Accession = accession.Trim(),
ProteinDescription = databaseSearchResult.ProteinDescription
};
var peptideEvidence = new SimpleMZIdentMLReader.PeptideEvidence
{
DbSeq = dbSequence,
Pre = databaseSearchResult.Pre,
Post = databaseSearchResult.Post,
PeptideRef = identification.Peptide,
Start = databaseSearchResult.Start,
End = databaseSearchResult.End,
};
identification.PepEvidence.Add(peptideEvidence);
}
simpleMzIdentMLData.Identifications.Add(identification);
}
return(simpleMzIdentMLData);
}
