public void ProteinAnnCombineSequenceEntries()
{
List <Protein> ok = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "xml2.xml"), true, DecoyType.None, null, false, null, out Dictionary <string, Modification> un);
List <Protein> destination = new List <Protein> {
new Protein("MKTCYYELLGVETHASDLELKKAYRKKALQYHPDKNPDNVEEATQKFAVIRAAYEVLSDPQERAWYDSHKEQILNDTPPSTDDYYDYEVDATVTGVTTDELLLFFNSALYTKIDNSAAGIYQIAGKIFAKLAKDEILSGKRLGKFSEYQDDVFEQDINSIGYLKACDNFINKTDKLLYPLFGYSPTDYEYLKHFYKTWSAFNTLKSFSWKDEYMYSKNYDRRTKREVNRRNEKARQQARNEYNKTVKRFVVFIKKLDKRMKEGAKIAEEQRKLKEQQRKNELNNRRKFGNDNNDEEKFHLQSWQTVKEENWDELEKVYDNFGEFENSKNDKEGEVLIYECFICNKTFKSEKQLKNHINTKLHKKNMEEIRKEMEEENITLGLDNLSDLEKFDSADESVKEKEDIDLQALQAELAEIERKLAESSSEDESEDDNLNIEMDIEVEDVSSDENVHVNTKNKKKRKKKKKAKVDTETEESESFDDTKDKRSNELDDLLASLGDKGLQTDDDEDWSTKAKKKKGKQPKKNSKSTKSTPSLSTLPSSMSPTSAIEVCTTCGESFDSRNKLFNHVKIAGHAAVKNVVKRKKVKTKRI",
"Acc1", organism: "H**o sapiens", geneNames: new List <Tuple <string, string> > {
new Tuple <string, string>("primary", "gene1")
},
name: "name1", fullName: "fullname1"),
new Protein("MKTCYYELLGVETHASDLELKKAYRKKALQYHPDKNPDNVEEATQKFAVIRAAYEVLSDPQERAWYDSHKEQILNDTPPSTDDYYDYEVDATVTGVTTDELLLFFNSALYTKIDNSAAGIYQIAGKIFAKLAKDEILSGKRLGKFSEYQDDVFEQDINSIGYLKACDNFINKTDKLLYPLFGYSPTDYEYLKHFYKTWSAFNTLKSFSWKDEYMYSKNYDRRTKREVNRRNEKARQQARNEYNKTVKRFVVFIKKLDKRMKEGAKIAEEQRKLKEQQRKNELNNRRKFGNDNNDEEKFHLQSWQTVKEENWDELEKVYDNFGEFENSKNDKEGEVLIYECFICNKTFKSEKQLKNHINTKLHKKNMEEIRKEMEEENITLGLDNLSDLEKFDSADESVKEKEDIDLQALQAELAEIERKLAESSSEDESEDDNLNIEMDIEVEDVSSDENVHVNTKNKKKRKKKKKAKVDTETEESESFDDTKDKRSNELDDLLASLGDKGLQTDDDEDWSTKAKKKKGKQPKKNSKSTKSTPSLSTLPSSMSPTSAIEVCTTCGESFDSRNKLFNHVKIAGHAAVKNVVKRKKVKTKRI",
"Acc2", organism: "H**o sapiens", geneNames: new List <Tuple <string, string> > {
new Tuple <string, string>("primary", "gene2")
},
name: "name2", fullName: "fullname2"),
new Protein("MNOTTHESAMESEQ",
"Acc2", organism: "H**o sapiens", geneNames: new List <Tuple <string, string> > {
new Tuple <string, string>("primary", "gene2")
},
name: "name2", fullName: "fullname2"),
};
List <Protein> newProteins = ProteinAnnotation.CombineAndAnnotateProteins(ok, destination);
Assert.AreEqual(2, newProteins.Count); // two were combined
Assert.IsTrue(newProteins.Any(p => p.Name.Contains(destination[0].Name) && p.Name.Contains(destination[1].Name)));
}
public void ProteinAnnTransferExactSequenceMatchMods()
{
List <Modification> mods = ProteinAnnotation.GetUniProtMods(TestContext.CurrentContext.TestDirectory);
List <Protein> ok = ProteinDbLoader.LoadProteinXML(Path.Combine(TestContext.CurrentContext.TestDirectory, "TestData", "xml2.xml"), true, DecoyType.None, mods, false, null, out Dictionary <string, Modification> un);
List <Protein> destination = new List <Protein> {
new Protein("MKTCYYELLGVETHASDLELKKAYRKKALQYHPDKNPDNVEEATQKFAVIRAAYEVLSDPQERAWYDSHKEQILNDTPPSTDDYYDYEVDATVTGVTTDELLLFFNSALYTKIDNSAAGIYQIAGKIFAKLAKDEILSGKRLGKFSEYQDDVFEQDINSIGYLKACDNFINKTDKLLYPLFGYSPTDYEYLKHFYKTWSAFNTLKSFSWKDEYMYSKNYDRRTKREVNRRNEKARQQARNEYNKTVKRFVVFIKKLDKRMKEGAKIAEEQRKLKEQQRKNELNNRRKFGNDNNDEEKFHLQSWQTVKEENWDELEKVYDNFGEFENSKNDKEGEVLIYECFICNKTFKSEKQLKNHINTKLHKKNMEEIRKEMEEENITLGLDNLSDLEKFDSADESVKEKEDIDLQALQAELAEIERKLAESSSEDESEDDNLNIEMDIEVEDVSSDENVHVNTKNKKKRKKKKKAKVDTETEESESFDDTKDKRSNELDDLLASLGDKGLQTDDDEDWSTKAKKKKGKQPKKNSKSTKSTPSLSTLPSSMSPTSAIEVCTTCGESFDSRNKLFNHVKIAGHAAVKNVVKRKKVKTKRI",
"")
};
Assert.AreEqual(ok[0].BaseSequence, destination[0].BaseSequence);
List <Protein> newProteins = ProteinAnnotation.CombineAndAnnotateProteins(ok, destination);
Assert.AreEqual(1, newProteins.Count);
Assert.AreEqual(ok[0].BaseSequence, newProteins[0].BaseSequence);
Assert.AreEqual(ok[0].OneBasedPossibleLocalizedModifications, newProteins[0].OneBasedPossibleLocalizedModifications);
Assert.IsTrue(newProteins[0].OneBasedPossibleLocalizedModifications.Keys.Count == 2);
Assert.IsTrue(ok[0].DatabaseReferences.All(x => newProteins[0].DatabaseReferences.Contains(x)));
Assert.IsTrue(ok[0].ProteolysisProducts.All(x => newProteins[0].ProteolysisProducts.Contains(x)));
}
public void Test1()
{
var mods = ProteinAnnotation.GetUniProtMods(Environment.CurrentDirectory);
Assert.Greater(mods.Count, 0);
}
