static void Main(string[] args)
{
Console.WriteLine("************MTDB Creator************");
Console.WriteLine("-> Creating Database");
Parser.Default.ParseArguments(args, CommandOptions);
MtdbCreator.CreateDB(ReadMzidList(), CommandOptions.DatabasePath);
Console.WriteLine("MTDB Creator Complete!");
}
/// <summary>
/// Read a MTDB Creator results file asynchronously.
/// </summary>
/// <param name="modIgnoreList">Ignores modifications contained in this list.</param>
/// <param name="progress">The progress reporter.</param>
/// <returns>The Protein-Spectrum-Match identifications.</returns>
public async Task <IEnumerable <PrSm> > ReadAsync(IEnumerable <string> modIgnoreList = null, IProgress <double> progress = null)
{
var prsms = new List <PrSm>();
if (!File.Exists(filePath))
{
return(prsms);
}
var database = await Task.Run(() => MtdbCreator.LoadDB(filePath));
foreach (var target in database.ConsensusTargets)
{
foreach (var id in target.Evidences)
{
// Degan: attempting to make it recognize the proteins from .mtdb format
foreach (var prot in id.Proteins)
{
var strippedSequence = target.Sequence;
strippedSequence = strippedSequence.Remove(0, 2);
strippedSequence = strippedSequence.Remove(strippedSequence.Length - 2, 2);
var entry = new PrSm {
Sequence = new Sequence(strippedSequence, new AminoAcidSet())
};
var rawSequence = target.Sequence;
var offset = target.Sequence.IndexOf('.');
var length = target.Sequence.Length;
foreach (var ptm in id.Ptms)
{
var position = rawSequence.Length - (length - (ptm.Location + offset));
var symbol = string.Empty;
// We only need to add the sign on positive values - the '-' is automatic on negative values
if (ptm.Mass >= 0)
{
symbol = "+";
}
rawSequence = rawSequence.Insert(position + 1, symbol + ptm.Mass);
var modComposition = Composition.ParseFromPlainString(ptm.Formula);
var mod = IcParameters.Instance.RegisterModification(ptm.Name, modComposition);
entry.Sequence[ptm.Location - 1] = new ModifiedAminoAcid(entry.Sequence[ptm.Location - 1], mod);
}
// Degan: attempting to make it recognize the proteins from .mtdb format
entry.ProteinName = prot.ProteinName;
// Degan: choosing stripped sequence rather than the raw sequence to exclude prior and successive amino acid
entry.SequenceText = strippedSequence;
entry.Charge = id.Charge;
entry.Scan = id.Scan;
prsms.Add(entry);
}
}
}
return(prsms);
}
