public static void TestDownloadListOfColumnsAvailableAtUniProt()
{
var uniProtColumnDictionary = ProteinDbRetriever.UniprotColumnsList();
Assert.IsTrue(uniProtColumnDictionary.Keys.Contains("Entry"));
Assert.AreEqual("id", uniProtColumnDictionary["Entry"]);
}
public static void TestDownloadAvailableUniProtProteomes()
{
string filepath = Path.Combine(TestContext.CurrentContext.TestDirectory, @"DatabaseTests");
string downloadedFilePath = ProteinDbRetriever.DownloadAvailableUniProtProteomes(filepath);
Assert.AreEqual(filepath + "\\availableUniProtProteomes.txt.gz", downloadedFilePath);
Dictionary <string, string> uniprotProteoms = ProteinDbRetriever.UniprotProteomesList(downloadedFilePath);
Assert.IsTrue(uniprotProteoms.Keys.Contains("UP000005640"));
Assert.AreEqual("H**o sapiens (Human)", uniprotProteoms["UP000005640"]);
File.Delete(downloadedFilePath);
//return null for bad filepath
filepath = "bubba";
downloadedFilePath = ProteinDbRetriever.DownloadAvailableUniProtProteomes(filepath);
Assert.IsNull(downloadedFilePath);
//bad file path returns null
uniprotProteoms = ProteinDbRetriever.UniprotProteomesList("badFilePath");
Assert.IsNull(uniprotProteoms);
//wrong file extension returns null
uniprotProteoms = ProteinDbRetriever.UniprotProteomesList(Path.Combine(TestContext.CurrentContext.TestDirectory, "DatabaseTests", @"bad.fasta"));
Assert.IsNull(uniprotProteoms);
}
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);
}
private static void LoadAvailableProteomes()
{
AvailableUniProtProteomes = ProteinDbRetriever.UniprotProteomesList(Path.Combine(DataDir, @"Proteomes", @"availableUniProtProteomes.txt.gz"));
}
