public static string TransferModifications(string sourceXmlPath, string destinationXmlPath)
{
var uniprotPtms = ProteinAnnotation.GetUniProtMods(Environment.CurrentDirectory);
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) + ".fasta");
var prot = newProts.FirstOrDefault(p => p.Accession.Contains("_"));
ProteinDbWriter.WriteFastaDatabase(newProts.SelectMany(p => p.GetVariantProteins()).ToList(), outfasta, "|");
return(outxml);
}
public static string TransferModifications(string sourceXmlPath, string destinationXmlPath)
{
var uniprotPtms = ProteinAnnotation.GetUniProtMods(Environment.CurrentDirectory);
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 = destinationXmlPath.EndsWith(".xml") | destinationXmlPath.EndsWith(".xml.gz") ?
ProteinDbLoader.LoadProteinXML(destinationXmlPath, true, DecoyType.None, uniprotPtms, false, null, out un).Select(p => p.NonVariantProtein).Distinct() :
ProteinDbLoader.LoadProteinFasta(destinationXmlPath, true, DecoyType.None, false, ProteinDbLoader.UniprotAccessionRegex, PgmNameRegex, PgmNameRegex, ProteinDbLoader.UniprotGeneNameRegex, ProteinDbLoader.UniprotOrganismRegex, out var un2).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) + ".fasta");
string outfastaWithDecoys = Path.Combine(Path.GetDirectoryName(destinationXmlPath), Path.GetFileNameWithoutExtension(destinationXmlPath) + ".withdecoys.fasta");
var prot = newProts.FirstOrDefault(p => p.Accession.Contains("_"));
var protsForFasta = newProts.SelectMany(p => p.GetVariantProteins()).Where(p => !p.BaseSequence.EndsWith('?')).ToList();
var decoyProtsForFasta = ProteinDbLoader.LoadProteinXML(destinationXmlPath, true, DecoyType.Reverse, uniprotPtms, false, null, out un).Where(p => !p.BaseSequence.EndsWith('?')).ToList();
ProteinDbWriter.WriteFastaDatabase(protsForFasta, outfasta, "|");
ProteinDbWriter.WriteFastaDatabase(decoyProtsForFasta, outfastaWithDecoys, "|");
File.WriteAllLines(outfastaWithDecoys, File.ReadAllLines(outfastaWithDecoys).Select(line => line.Replace("mz|DECOY_", "rev_mz|")));
return(outxml);
}