static void Main(string[] args)
{
string strPath = Environment.GetFolderPath(Environment.SpecialFolder.DesktopDirectory);
string[] files = Directory.GetFiles(strPath + @"\Rosalind", "*.txt"); //Assumes only one txt file in this directory - the data set
string[] lines = { "" };
foreach (string file in files)
{
lines = File.ReadAllLines(file);
}
List <Fasta> fastaList = Fasta.DecodeFasta(lines);
string[] dnaStrings = new string[fastaList.Count];
for (int i = 0; i < fastaList.Count; i++)
{
dnaStrings[i] = fastaList[i].DNA;
}
string[] introns = dnaStrings.Skip(1).ToArray();
for (int i = 0; i < introns.Length; i++)
{
introns[i] = introns[i].Replace('T', 'U');
}
Console.WriteLine(TranscribeRNAToProtein(dnaStrings[0].Replace('T', 'U'), introns));
Console.ReadLine();
}
static void Main(string[] args)
{
string strPath = Environment.GetFolderPath(Environment.SpecialFolder.DesktopDirectory);
string[] files = Directory.GetFiles(strPath + @"\Rosalind", "*.txt"); //Assumes only one txt file in this directory - the data set
string[] lines = { "" };
foreach (string file in files)
{
lines = File.ReadAllLines(file);
}
List <Fasta> fastaList = Fasta.DecodeFasta(lines);
string[] strings = new string[fastaList.Count];
for (int i = 0; i < fastaList.Count; i++)
{
strings[i] = fastaList[i].DNA;
}
ProfileMatrix matrix = new ProfileMatrix(strings);
Console.WriteLine(matrix.ConsensusString);
ProfileMatrix.OutputProfileMatrix(matrix);
Console.ReadLine();
}
static void Main(string[] args)
{
string strPath = Environment.GetFolderPath(Environment.SpecialFolder.DesktopDirectory);
string[] files = Directory.GetFiles(strPath + @"\Rosalind", "*.txt"); //Assumes only one txt file in this directory - the data set
string[] lines = { "" };
lines = File.ReadAllLines(files[0]);
List <Fasta> fastas = Fasta.DecodeFasta(lines);
Stopwatch itime = new Stopwatch();
string[] dnaOnly = new string[fastas.Count];
for (int i = 0; i < fastas.Count; i++)
{
dnaOnly[i] = fastas[i].DNA;
}
itime.Start();
Console.WriteLine(LongestCommonSubstring(dnaOnly.ToList()));
itime.Stop();
Console.WriteLine("Took: {0}ms", itime.ElapsedMilliseconds);
Console.ReadLine();
}
static void Main(string[] args)
{
string strPath = Environment.GetFolderPath(Environment.SpecialFolder.DesktopDirectory);
string[] files = Directory.GetFiles(strPath + @"\Rosalind", "*.txt"); //Assumes only one txt file in this directory - the data set
string[] lines = { "" };
foreach (string file in files)
{
lines = File.ReadAllLines(file);
}
Regex regex = new Regex(@"N[^P][ST][^P]", RegexOptions.Multiline);
string url = @"http://www.uniprot.org/uniprot/";
List <(string id, int[] positions)> tuples = new List <(string id, int[] positions)>();
foreach (string protein in lines)
{
List <int> positions = new List <int>();
(string id, int[] positions)tuple;
tuple.id = protein;
string html = MakeGetRequest(url + protein + ".fasta");
Fasta fasta = Fasta.DecodeFasta(html.Split('\n'))[0];
for (int i = 0; i < fasta.DNA.Length - 4; i++)
{
if (regex.IsMatch(fasta.DNA.Substring(i, 4)))
{
positions.Add(i + 1);
}
}
if (positions.Count != 0)
{
tuple.positions = positions.ToArray();
tuples.Add(tuple);
}
}
for (int i = 0; i < tuples.Count; i++)
{
if (tuples[i].positions.Length != 0)
{
Console.WriteLine(tuples[i].id);
tuples[i].positions.ToList().ForEach(s => Console.Write(s + " "));
Console.WriteLine();
}
}
Console.ReadLine();
}
static void Main(string[] args)
{
string strPath = Environment.GetFolderPath(Environment.SpecialFolder.DesktopDirectory);
string[] files = Directory.GetFiles(strPath + @"\Rosalind", "*.txt"); //Assumes only one txt file in this directory - the data set
string[] lines = { "" };
foreach (string file in files)
{
lines = File.ReadAllLines(file);
}
Fasta fasta = Fasta.DecodeFasta(lines)[0];
List <string> proteins = ReadFrames(fasta.DNA);
proteins.ForEach((s) => Console.WriteLine(s));
Console.ReadLine();
}
static void Main(string[] args)
{
string strPath = Environment.GetFolderPath(Environment.SpecialFolder.DesktopDirectory);
string[] files = Directory.GetFiles(strPath + @"\Rosalind", "*.txt"); //Assumes only one txt file in this directory - the data set
string[] lines = { "" };
foreach (string file in files)
{
lines = File.ReadAllLines(file);
}
Fasta fasta = Fasta.DecodeFasta(lines)[0];
int?[][] palindromes = FindDNAReversePalindrome(fasta.DNA, 4, 12);
Console.WriteLine();
Console.ReadLine();
}