public static void TestRetrieveUniProtProteome()
{
string filepath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"DatabaseTests");
//UP000008595 is Uukuniemi virus (strain S23) (Uuk) which only has 4 proteins
string returnedFilePath = ProteinDbRetriever.RetrieveProteome("UP000008595", filepath, ProteinDbRetriever.ProteomeFormat.fasta, ProteinDbRetriever.Reviewed.yes, ProteinDbRetriever.Compress.yes, ProteinDbRetriever.IncludeIsoforms.yes);
filepath += "\\UP000008595_reviewed_isoform.fasta.gz";
Assert.AreEqual(filepath, returnedFilePath);
Assert.IsTrue(File.Exists(filepath));
var proteinList = ProteinDbLoader.LoadProteinFasta(filepath, true, DecoyType.None, false, out var dbErrors, ProteinDbLoader.UniprotAccessionRegex, ProteinDbLoader.UniprotFullNameRegex,
ProteinDbLoader.UniprotFullNameRegex, ProteinDbLoader.UniprotGeneNameRegex, ProteinDbLoader.UniprotOrganismRegex);
Assert.AreEqual(4, proteinList.Count);
Assert.IsTrue(proteinList.Select(p => p.Accession).ToList().Contains("P33453"));
Assert.AreEqual("MLLAICSRTIRQQGLNCPPAVTFTSSHMRPPIPSFLLWTEGSDVLMDFDLDTIPAGSVTGSSIGPKFKIKTQAASSFVHDFTFAHWCDASDMPLRDHFPLVNDTFDHWTPDFISQRLDGSKVVVEFTTNRSDQEQSLISAFNTKVGKYEVALHNRSTTSSILFGVVV" +
"VSETTVVTNLNLNQQEVDELCFRFLVARAVHLEMTTKMIIPEYDDEDEDKRSREVKAAFHSVQPDWNVTEANFAPFSRRMFSNFAQMEPDKEYLAHIILDSLKQAQADLDGNHYLNESLTEQARLDRNREESLNMVKDFERDFNNAAQRSAWSHKSTVPFPGVIPKVSGDTTSLSRLVEL" +
"PVITGGSDATIRAWRSAYGSVSNGTVERCDEDVERERRAALCSLTVEELEESKALRMKYHRCKIDNGMMDKLDLAMQGVEAKEFKNHPSIIKKRSKSKKTFPLTADTRDIDLFLHHDDLMFNNEHSQTPPAAMIEAVKAGADAQSLHGLDKSANPWYASALWFLGLPIGLWLFMCTCIGVEL" +
"SISLKQHCGRQKFIIKKLRFFDIFLLIKPTNSGSHVFYSIAFPESAILGKLHRSQCFKGLQFEDGWFWTEFSSFKMSKLTNVVKCLSTGFNLFWFWRDYYEVPFWAGNEKDFQTGKQRANKMFKFCLLMLLEDKARTEEIATLSRYVMMEGFVSPPCIPKPQKMIEKLPNLARTKFQVWLISR" +
"MLQTIIRVSDYPFKITAGHKSANWTGMFNWVTGEPIESTQKLISLFYLGYLKNKEESPERNASIGMYKKILEYEDKHPGRYTYLGLGDPPSDDTRFHEYSISLLKHLCIHAEHDLRRNWGESFKAMISRDIVDAIASLDLERLATLKASSNFNEEWYQKRGDGKTYHRSKVLEKVSKYVKKSSSH" +
"VHHIMEECLRKVESQGCMHVCLFKKPQHGGLREIYVLGFEERVVQLVIETIARQICKRFKSETLTNPKQKLAIPETHGLRAVKTCGIHHETVATSDDAAKWNQCHHVTKFALMLCHFTDPLFHGFIIRGCSMFMKKRIMIDQSLIDIIDSHTTLETSDAYLQKIHRGYHGSLDDQPRWISRGGAFVQ" +
"TETGMMQGILHYTSSLLHTLLQEWLRTFSQRFIRTRVSVDQRPDVLVDVLQSSDDSGMMISFPSTDKGATGKYRYLSALIFKYKKVIGKYLGIYSSVKSTNNTLHLLEFNSEFFFHINHNRPLLRWITACDTISEQESLASRQEEMYNNLTSVLEGGGSFSLVSFCQFGQLLLHYTLLGMTVSPLFLEY" +
"IKLVSEIKDPSLGYFLMDHPFGSGLSGFKYNVWVAVQNSILGSRYRSLLEAIQNSDSAAPKKTLDTTTSGTFVQSTIIRFGDRKKWQRLVDRLNLPEDWLDVIDKNPEIVYRRPRDGFEVSLRIAEKVHSPGVSNSLSKGNCIIRVISSSVYILSRSILSDGLAWLYDEEEEVKRPLLYKVMNQPELDLHSRLTPA" +
"QLSTLFPMMAEFEKLQTHLRSYMKIEGEFISKKKVITQTRVNILETERFLRARPEDLIADKWFGFTRTRMTPRTFKEEWENLTSVFPWLTGNPSETLELSPFQHHVQLRNFFSRLDLKGRDIRIIGAPIKKSSGVSNVSTAIRDNFFPRFVLTHIPDEAAMERIEAAGILKHALFLTVTGPYTDQSKLDMCRDF" +
"ITSSEPITLKPNHGKTRTNVLSLFQDYFSKRGPDIIFNRIQMANCGVIGGFTSPQKPKEVDGKIVYTGDGVWRGIVDGFQIQLVITYMPKQKSNELKSITVNSDRCISALSSFCQSWCKEMGVFNTEDFSKTQRFSKASFFMHKFKISGSKQTLGAPIFIVSEKIFRPICWDPSKLEFRVRGNTLNLTY" +
"KEVNPGAGQRMFNILSYTVKDTDVSDENAFKLMSLSPRHKFHGREPSTSWICMRALPISTIDKLLERILNRERISGSIDNERLAECFKNVMESTLRRKGVFLSEFSRATQKMLDGLSRDMLDFFAEAGLNDDLLLEEEPWLSGLDTFMLDDEAYLEEYNLGPFGVFSVEQEMNTKYYHHLLLD" +
"SLVEDVIQKLSLDGLRKLFQEEEAPLEYKKEVIRLLNILQRDASQIKWKSRDLLSENMGLDVDDDMFG", proteinList.Where(p => p.Accession == "P33453").FirstOrDefault().BaseSequence);
File.Delete(filepath);
//fasta; unreviewed; non-compressed; no isoforms
filepath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"DatabaseTests");
returnedFilePath = ProteinDbRetriever.RetrieveProteome("UP000008595", filepath, ProteinDbRetriever.ProteomeFormat.fasta, ProteinDbRetriever.Reviewed.no, ProteinDbRetriever.Compress.no, ProteinDbRetriever.IncludeIsoforms.no);
filepath += "\\UP000008595_unreviewed.fasta";
Assert.AreEqual(filepath, returnedFilePath);
Assert.IsTrue(File.Exists(filepath));
File.Delete(filepath);
//xml; reviewed; compresseded; no isoforms
filepath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"DatabaseTests");
returnedFilePath = ProteinDbRetriever.RetrieveProteome("UP000008595", filepath, ProteinDbRetriever.ProteomeFormat.xml, ProteinDbRetriever.Reviewed.yes, ProteinDbRetriever.Compress.yes, ProteinDbRetriever.IncludeIsoforms.no);
filepath += "\\UP000008595_reviewed.xml.gz";
Assert.AreEqual(filepath, returnedFilePath);
Assert.IsTrue(File.Exists(filepath));
File.Delete(filepath);
//xml; unreviewed; non-compresseded; no isoforms
filepath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"DatabaseTests");
returnedFilePath = ProteinDbRetriever.RetrieveProteome("UP000008595", filepath, ProteinDbRetriever.ProteomeFormat.xml, ProteinDbRetriever.Reviewed.no, ProteinDbRetriever.Compress.no, ProteinDbRetriever.IncludeIsoforms.no);
filepath += "\\UP000008595_unreviewed.xml";
Assert.AreEqual(filepath, returnedFilePath);
Assert.IsTrue(File.Exists(filepath));
File.Delete(filepath);
//junk null return
filepath = "pathDoesNotExists";
returnedFilePath = ProteinDbRetriever.RetrieveProteome("UP000008595", filepath, ProteinDbRetriever.ProteomeFormat.xml, ProteinDbRetriever.Reviewed.no, ProteinDbRetriever.Compress.no, ProteinDbRetriever.IncludeIsoforms.no);
filepath += "\\UP000008595_unreviewed.xml";
Assert.IsNull(returnedFilePath);
//we don't support filetypes other than fasta or xml currently
//requesting gff or other file formats will return null for now.
filepath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"DatabaseTests");
returnedFilePath = ProteinDbRetriever.RetrieveProteome("UP000008595", filepath, ProteinDbRetriever.ProteomeFormat.gff, ProteinDbRetriever.Reviewed.no, ProteinDbRetriever.Compress.no, ProteinDbRetriever.IncludeIsoforms.no);
filepath += "\\UP000008595_unreviewed.xml";
Assert.IsNull(returnedFilePath);
}
public static void ClassCleanup()
{
File.Delete(@"TestFiles\AttackAnimKits_Test.dbc");
File.Delete(@"TestFiles\CharacterFacialHairStyles_Test.dbc");
File.Delete(@"TestFiles\WowError_Strings_Test.dbc");
}
public void FilesLoading() //delete mzLib\Test\bin\x64\Debug to update your local unimod list
{
Loaders.LoadElements();
string uniModPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "unimod_tables2.xml");
string psiModPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "PSI-MOD.obo2.xml");
string uniProtPath = Path.Combine(TestContext.CurrentContext.TestDirectory, "ptmlist2.txt");
// UniModPTMs
var unimodMods = Loaders.LoadUnimod(uniModPath).ToList();
Assert.AreEqual(2702, unimodMods.Count); // UniMod PTM list may be updated at some point, causing the unit test to fail
List <Modification> myList = unimodMods.Where(m => m.OriginalId.Equals("HexNAc(2)")).ToList();
Modification testMod = myList.First();
int neutralLossCount = 0;
if (testMod.NeutralLosses.Count != 0)
{
foreach (KeyValuePair <MassSpectrometry.DissociationType, List <double> > item in testMod.NeutralLosses)
{
foreach (double loss in item.Value)
{
neutralLossCount++;
}
}
}
Assert.AreEqual(2, neutralLossCount);
// PsiMod PTMs
var psiModDeserialized = Loaders.LoadPsiMod(psiModPath);
// N6,N6,N6-trimethyllysine
var trimethylLysine = psiModDeserialized.Items.OfType <UsefulProteomicsDatabases.Generated.oboTerm>().First(b => b.id.Equals("MOD:00083"));
Assert.AreEqual("1+", trimethylLysine.xref_analog.First(b => b.dbname.Equals("FormalCharge")).name);
// Phosphoserine
Assert.IsFalse(psiModDeserialized.Items.OfType <UsefulProteomicsDatabases.Generated.oboTerm>().First(b => b.id.Equals("MOD:00046")).xref_analog.Any(b => b.dbname.Equals("FormalCharge")));
Dictionary <string, int> formalChargesDictionary = Loaders.GetFormalChargesDictionary(psiModDeserialized);
// UniProt PTMs
var uniprotPtms = Loaders.LoadUniprot(uniProtPath, formalChargesDictionary).ToList();
Assert.LessOrEqual(300, uniprotPtms.Count()); // UniProt PTM list may be updated at some point, causing the unit test to fail
// write UniProt and UniMod PTMs to a file
using (StreamWriter w = new StreamWriter(Path.Combine(TestContext.CurrentContext.TestDirectory, "test.txt")))
{
foreach (var nice in uniprotPtms)
{
w.WriteLine(nice.ToString());
w.WriteLine("//");
}
foreach (var nice in unimodMods)
{
w.WriteLine(nice.ToString());
w.WriteLine("//");
}
}
// read in the file and make sure that it has the same number of PTMs
var sampleModList = PtmListLoader.ReadModsFromFile(Path.Combine(TestContext.CurrentContext.TestDirectory, "test.txt"), out var errors).ToList();
Assert.AreEqual(uniprotPtms.Count + unimodMods.Count, sampleModList.Count());
List <Modification> myOtherList = new List <Modification>();
foreach (Modification mod in sampleModList)
{
if (mod.IdWithMotif != null && mod.IdWithMotif.Contains("Acetyl"))
{
myOtherList.Add(mod);
}
}
var thisMod = myOtherList.First();
Assert.IsTrue(thisMod.MonoisotopicMass > 42);
Assert.IsTrue(thisMod.MonoisotopicMass < 43);
File.Delete(uniModPath);
File.Delete(psiModPath);
File.Delete(uniProtPath);
}