public static void TestStringSanitation()
{
string messedUpSequence = @"PRO�EIN�";
// just test the string sanitation method alone
var sanitized = ProteinDbLoader.SanitizeAminoAcidSequence(messedUpSequence, 'X');
Assert.That(sanitized == "PROXEINX");
// test reading from a fasta
Protein protein = new Protein(messedUpSequence, "accession");
string fastaPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", @"messedUp.fasta");
ProteinDbWriter.WriteFastaDatabase(new List <Protein> {
protein
}, fastaPath, "|");
var fastaProteins = ProteinDbLoader.LoadProteinFasta(fastaPath, true, DecoyType.Reverse, false, ProteinDbLoader.UniprotAccessionRegex,
ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotNameRegex, ProteinDbLoader.UniprotGeneNameRegex,
ProteinDbLoader.UniprotOrganismRegex, out var a);
Assert.That(fastaProteins.First(p => !p.IsDecoy).BaseSequence == "PROXEINX");
// digest and fragment to check that there isn't a crash
var peptides = fastaProteins.First().Digest(new DigestionParams(), new List <Modification>(), new List <Modification>()).ToList();
foreach (PeptideWithSetModifications peptide in peptides)
{
List <Product> fragments = new List <Product>();
peptide.Fragment(DissociationType.HCD, FragmentationTerminus.Both, fragments);
}
// test reading from an XML
string xmlPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", @"messedUp.xml");
ProteinDbWriter.WriteXmlDatabase(new Dictionary <string, HashSet <Tuple <int, Modification> > >(), new List <Protein> {
protein
}, xmlPath);
var xmlProteins = ProteinDbLoader.LoadProteinXML(xmlPath, true, DecoyType.Reverse, new List <Modification>(), false, new List <string>(), out var unk);
Assert.That(xmlProteins.First(p => !p.IsDecoy).BaseSequence == "PROXEINX");
}
