Пример #1
0
        public void TestMultipleSequencesInFile()
        {
            var expectedData = new[]
            {
                Tuple.Create("E3MFGYR02JWQ7T", 265),
                Tuple.Create("E3MFGYR02JA6IL", 271),
                Tuple.Create("E3MFGYR02JHD4H", 310),
                Tuple.Create("E3MFGYR02GFKUC", 299),
                Tuple.Create("E3MFGYR02FTGED", 281),
                Tuple.Create("E3MFGYR02FR9G7", 261),
                Tuple.Create("E3MFGYR02GAZMS", 278),
                Tuple.Create("E3MFGYR02HHZ8O", 221),
                Tuple.Create("E3MFGYR02GPGB1", 269),
                Tuple.Create("E3MFGYR02F7Z7G", 219),
            };

            SFFParser parser = new SFFParser();

            using (parser.Open(filePath))
            {
                int index = 0;
                foreach (var sequence in parser.Parse())
                {
                    Assert.IsTrue(expectedData.Length > index);
                    Assert.AreEqual(expectedData[index].Item1, sequence.ID);
                    Assert.AreEqual(expectedData[index].Item2, sequence.Count);
                    index++;
                }
            }
        }
Пример #2
0
 public void TestSffWhenParsingOneOfMany()
 {
     using (SFFParser parser = new SFFParser(filePath))
     {
         var sequence = parser.Parse().FirstOrDefault();
         Assert.IsNotNull(sequence);
         Assert.AreEqual(265, sequence.Count);
     }
 }
Пример #3
0
        public void TestSffForOneSequence()
        {
            string expectedSequence =
                "TCAGGGTCTACATGTTGGTTAACCCGTACTGATTTGAATTGGCTCTTTGTCTTTCCAAAGGGAATTCATCTTCTTATGGC" +
                "ACACATAAAGGATAAATACAAGAATCTTCCTATTTACATCACTGAAAATGGCATGGCTGAATCAAGGAATGACTCAATAC" +
                "CAGTCAATGAAGCCCGCAAGGATAGTATAAGGATTAGATACCATGATGGCCATCTTAAATTCCTTCTTCAAGCGATCAAG" +
                "GAAGGTGTTAATTTGAAGGGGCTTA";

            using (SFFParser parser = new SFFParser(filePath))
            {
                var sequence = parser.Parse().FirstOrDefault();
                Assert.IsNotNull(sequence);
                Assert.IsInstanceOfType(sequence, typeof(QualitativeSequence));
                Assert.AreEqual(265, sequence.Count);

                string actualSequence = new string(sequence.Select(b => (char)b).ToArray());
                Assert.AreEqual(expectedSequence, actualSequence);
                Assert.AreEqual(sequence.Alphabet, Alphabets.DNA);
                Assert.AreEqual("E3MFGYR02JWQ7T", sequence.ID);
            }
        }
Пример #4
0
        public void TestSffForOneSequence()
        {
            const string ExpectedSequence = "TCAGGGTCTACATGTTGGTTAACCCGTACTGATTTGAATTGGCTCTTTGTCTTTCCAAAGGGAATTCATCTTCTTATGGC" +
                                            "ACACATAAAGGATAAATACAAGAATCTTCCTATTTACATCACTGAAAATGGCATGGCTGAATCAAGGAATGACTCAATAC" +
                                            "CAGTCAATGAAGCCCGCAAGGATAGTATAAGGATTAGATACCATGATGGCCATCTTAAATTCCTTCTTCAAGCGATCAAG" +
                                            "GAAGGTGTTAATTTGAAGGGGCTTA";

            SFFParser parser = new SFFParser();

            using (parser.Open(filePath))
            {
                var sequence = parser.Parse().FirstOrDefault();
                Assert.IsNotNull(sequence);
                Assert.IsInstanceOf <QualitativeSequence>(sequence);
                Assert.AreEqual(265, sequence.Count);

                var actualSequence = sequence.ConvertToString();
                Assert.AreEqual(ExpectedSequence, actualSequence);
                Assert.AreEqual(sequence.Alphabet, Alphabets.DNA);
                Assert.AreEqual("E3MFGYR02JWQ7T", sequence.ID);
            }
        }