public void test_modification_transfer_exact_sequence_match()
{
var nice = new List <Modification>
{
new ModificationWithLocation("fayk", null, null, ModificationSites.A, null, null)
};
Dictionary <string, Modification> un;
List <Protein> ok = ProteinDbLoader.LoadProteinDb(Path.Combine(TestContext.CurrentContext.TestDirectory, @"xml2.xml"), false, nice, false, out un);
List <Protein> destination = new List <Protein> {
new Protein("MKTCYYELLGVETHASDLELKKAYRKKALQYHPDKNPDNVEEATQKFAVIRAAYEVLSDPQERAWYDSHKEQILNDTPPSTDDYYDYEVDATVTGVTTDELLLFFNSALYTKIDNSAAGIYQIAGKIFAKLAKDEILSGKRLGKFSEYQDDVFEQDINSIGYLKACDNFINKTDKLLYPLFGYSPTDYEYLKHFYKTWSAFNTLKSFSWKDEYMYSKNYDRRTKREVNRRNEKARQQARNEYNKTVKRFVVFIKKLDKRMKEGAKIAEEQRKLKEQQRKNELNNRRKFGNDNNDEEKFHLQSWQTVKEENWDELEKVYDNFGEFENSKNDKEGEVLIYECFICNKTFKSEKQLKNHINTKLHKKNMEEIRKEMEEENITLGLDNLSDLEKFDSADESVKEKEDIDLQALQAELAEIERKLAESSSEDESEDDNLNIEMDIEVEDVSSDENVHVNTKNKKKRKKKKKAKVDTETEESESFDDTKDKRSNELDDLLASLGDKGLQTDDDEDWSTKAKKKKGKQPKKNSKSTKSTPSLSTLPSSMSPTSAIEVCTTCGESFDSRNKLFNHVKIAGHAAVKNVVKRKKVKTKRI",
"", new Dictionary <int, List <Modification> >(), null, null, null, "", "", false, false, new List <GoTerm>())
};
Assert.AreEqual(ok[0].BaseSequence, destination[0].BaseSequence);
List <Protein> new_proteins = SequenceSimilarity.TransferModifications(ok, destination);
Assert.AreEqual(ok[0].OneBasedBeginPositions, new_proteins[0].OneBasedBeginPositions);
Assert.AreEqual(ok[0].OneBasedEndPositions, new_proteins[0].OneBasedEndPositions);
Assert.AreEqual(ok[0].OneBasedPossibleLocalizedModifications, new_proteins[0].OneBasedPossibleLocalizedModifications);
Assert.True(new_proteins[0].OneBasedPossibleLocalizedModifications.Keys.Count == 2);
Assert.AreEqual(ok[0].GoTerms.Count, new_proteins[0].GoTerms.Count);
Assert.AreEqual(ok[0].BaseSequence, new_proteins[0].BaseSequence);
Assert.AreEqual(1, new_proteins.Count);
}
public void test_read_Ensembl_pepAllFasta()
{
var nice = new List <Modification>
{
new ModificationWithLocation("fayk", null, null, ModificationSites.A, null, null)
};
Dictionary <string, Modification> un;
List <Protein> ok = ProteinDbLoader.LoadProteinDb(Path.Combine(TestContext.CurrentContext.TestDirectory, @"test_ensembl.pep.all.fasta"), false, nice, false, out un);
ProteinDbWriter.WriteXmlDatabase(new Dictionary <string, HashSet <Tuple <int, ModificationWithMass> > >(), ok, Path.Combine(TestContext.CurrentContext.TestDirectory, @"rewrite_test_ensembl.pep.all.xml"));
List <Protein> ok2 = ProteinDbLoader.LoadProteinDb(Path.Combine(TestContext.CurrentContext.TestDirectory, @"rewrite_test_ensembl.pep.all.xml"), false, nice, false, out un);
Assert.AreEqual(ok.Count, ok2.Count);
Assert.True(Enumerable.Range(0, ok.Count).All(i => ok[i].BaseSequence == ok2[i].BaseSequence));
Assert.AreEqual("ENSP00000381386", ok[0].Accession);
Assert.AreEqual("ENSP00000215773", ok[1].Accession);
Assert.AreEqual("pep:known chromosome:GRCh37:22:24313554:24316773:-1 gene:ENSG00000099977 transcript:ENST00000398344 gene_biotype:protein_coding transcript_biotype:protein_coding", ok[0].FullName);
Assert.AreEqual("pep:known chromosome:GRCh37:22:24313554:24322019:-1 gene:ENSG00000099977 transcript:ENST00000350608 gene_biotype:protein_coding transcript_biotype:protein_coding", ok[1].FullName);
Assert.True(ok.All(p => p.OneBasedBeginPositions.All(begin => begin == null || begin > 0 && begin <= p.Length)));
Assert.True(ok.All(p => p.OneBasedEndPositions.All(end => end == null || end > 0 && end <= p.Length)));
Assert.True(ok2.All(p => p.OneBasedBeginPositions.All(begin => begin == null || begin > 0 && begin <= p.Length)));
Assert.True(ok2.All(p => p.OneBasedEndPositions.All(end => end == null || end > 0 && end <= p.Length)));
}
public void test_read_write_read_fasta()
{
var nice = new List <Modification>
{
new ModificationWithLocation("fayk", null, null, ModificationSites.A, null, null)
};
Dictionary <string, Modification> un;
List <Protein> ok = ProteinDbLoader.LoadProteinDb(Path.Combine(TestContext.CurrentContext.TestDirectory, @"test_ensembl.pep.all.fasta"), false, nice, false, out un);
ProteinDbWriter.WriteFastaDatabase(ok, Path.Combine(TestContext.CurrentContext.TestDirectory, @"rewrite_test_ensembl.pep.all.fasta"));
List <Protein> ok2 = ProteinDbLoader.LoadProteinDb(Path.Combine(TestContext.CurrentContext.TestDirectory, @"rewrite_test_ensembl.pep.all.fasta"), false, nice, false, out un);
Assert.AreEqual(ok.Count, ok2.Count);
Assert.True(Enumerable.Range(0, ok.Count).All(i => ok[i].BaseSequence == ok2[i].BaseSequence));
Assert.True(ok.All(p => p.OneBasedBeginPositions.All(begin => begin == null || begin > 0 && begin <= p.Length)));
Assert.True(ok.All(p => p.OneBasedEndPositions.All(end => end == null || end > 0 && end <= p.Length)));
Assert.True(ok2.All(p => p.OneBasedBeginPositions.All(begin => begin == null || begin > 0 && begin <= p.Length)));
Assert.True(ok2.All(p => p.OneBasedEndPositions.All(end => end == null || end > 0 && end <= p.Length)));
}
static void Main(IDictionary<string, IList<Modification>> allKnownModifications)
{
List<Protein> proteins = ProteinDbLoader.LoadProteinDb("uniprot-proteome%3AUP000005640.xml-Jurkat_SAV_DBGPTMDproteinPruned.xml", allKnownModifications;
}
