public void TestSffWhenParsingOneOfMany()
{
SFFParser parser = new SFFParser();
using (parser.Open(filePath))
{
var sequence = parser.Parse().FirstOrDefault();
Assert.IsNotNull(sequence);
Assert.AreEqual(265, sequence.Count);
}
}
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);
}
}
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++;
}
}
}