Exemple #1
0
        public void OverlapGraphTest()
        {
            string input = @">Rosalind_0498
                             AAATAAA
                             >Rosalind_2391
                             AAATTTT
                             >Rosalind_2323
                             TTTTCCC
                             >Rosalind_0442
                             AAATCCC
                             >Rosalind_5013
                             GGGTGGG";

            var expected = new List <Tuple <string, string> > ()
            {
                Tuple.Create("Rosalind_0498", "Rosalind_2391"),
                Tuple.Create("Rosalind_0498", "Rosalind_0442"),
                Tuple.Create("Rosalind_2391", "Rosalind_2323")
            };

            var result = new List <Tuple <string, string> > (
                OverlapGrapher.calculateGraph(3, FASTA.read(new StringReader(input))));

            Assert.AreEqual(expected.Count, result.Count);

            foreach (var pair in expected.Zip(result, (a, b) => Tuple.Create(a, b)))
            {
                Assert.AreEqual(pair.Item1, pair.Item2);
            }
        }
Exemple #2
0
        private static void OverlapGraph(IDictionary <string, ValueObject> args)
        {
            string filename = args ["<filename>"].ToString();

            using (var infile = new FileStream(filename, FileMode.Open))
                using (var reader = new StreamReader(infile)) {
                    var result = OverlapGrapher.calculateGraph(3, FASTA.read(reader));
                    foreach (var pair in result)
                    {
                        Console.WriteLine("{0} {1}", pair.Item1, pair.Item2);
                    }
                }
        }