public List <string> TransferModifications(string spritzDirectory, string sourceXmlPath, List <string> destinationXmlPaths, List <Protein> additionalProteins)
{
var uniprotPtms = ProteinAnnotation.GetUniProtMods(spritzDirectory);
List <string> outxmls = new List <string>();
var uniprot = File.Exists(sourceXmlPath) ?
ProteinDbLoader.LoadProteinXML(sourceXmlPath, true, DecoyType.None, uniprotPtms, false, null, out Dictionary <string, Modification> un) :
new List <Protein>();
foreach (var xml in destinationXmlPaths)
{
if (xml == null || !File.Exists(xml))
{
continue;
}
string outxml = Path.Combine(Path.GetDirectoryName(xml), Path.GetFileNameWithoutExtension(xml) + ".withmods.xml");
var nonVariantProts = ProteinDbLoader.LoadProteinXML(xml, true, DecoyType.None, uniprotPtms, false, null, out un).Select(p => p.NonVariantProtein).Distinct();
var newProts = ProteinAnnotation.CombineAndAnnotateProteins(uniprot, nonVariantProts.Concat(additionalProteins).ToList());
ProteinDbWriter.WriteXmlDatabase(null, newProts, outxml);
string outfasta = Path.Combine(Path.GetDirectoryName(xml), Path.GetFileNameWithoutExtension(xml) + ".spritz.fasta");
ProteinDbWriter.WriteFastaDatabase(newProts.SelectMany(p => p.GetVariantProteins()).ToList(), outfasta, "|");
outxmls.Add(outxml);
}
return(outxmls);
}
public string TransferModifications(string spritzDirectory, string sourceXmlPath, string destinationXmlPath)
{
var uniprotPtms = ProteinAnnotation.GetUniProtMods(spritzDirectory);
var uniprot = ProteinDbLoader.LoadProteinXML(sourceXmlPath, true, DecoyType.None, uniprotPtms, false, null, out var un);
string outxml = Path.Combine(Path.GetDirectoryName(destinationXmlPath), Path.GetFileNameWithoutExtension(destinationXmlPath) + ".withmods.xml");
var nonVariantProts = ProteinDbLoader.LoadProteinXML(destinationXmlPath, true, DecoyType.None, uniprotPtms, false, null, out un).Select(p => p.NonVariantProtein).Distinct();
var newProts = ProteinAnnotation.CombineAndAnnotateProteins(uniprot, nonVariantProts.ToList());
ProteinDbWriter.WriteXmlDatabase(null, newProts, outxml);
string outfasta = Path.Combine(Path.GetDirectoryName(destinationXmlPath), Path.GetFileNameWithoutExtension(destinationXmlPath) + ".spritz.fasta");
var prot = newProts.FirstOrDefault(p => p.Accession.Contains("_"));
ProteinDbWriter.WriteFastaDatabase(newProts.SelectMany(p => p.GetVariantProteins()).ToList(), outfasta, "|");
return(outxml);
}
