//http://rosalind.info/problems/corr/
public ErrorCorrectionInReads()
{
string[] dnaStrings = FASTAToDictionary.Convert(File.ReadAllLines(@"C:\code\dataset.txt").ToList()).Values.ToArray();
var valid = new List <string>();
var invalid = new List <string>();
foreach (string dnaString in dnaStrings)
{
bool isValid = false;
string reverse = ComplementingAStrandOfDna.ReverseCompliment(dnaString, false);
for (int i = 0; i < valid.Count; i++)
{
if (dnaString.Equals(valid[i]) || reverse.Equals(valid[i]))
{
isValid = true;
break;
}
}
if (isValid)
{
continue;
}
for (int i = 0; i < invalid.Count; i++)
{
if (dnaString.Equals(invalid[i]) || reverse.Equals(invalid[i]))
{
valid.Add(dnaString);
valid.Add(reverse);
invalid.RemoveAt(i);
isValid = true;
break;
}
}
if (isValid == false)
{
invalid.Add(dnaString);
}
}
foreach (string inv in invalid)
{
foreach (var val in valid)
{
if (CountingPointMutations.GetHammingDistance(inv, val) == 1)
{
Console.WriteLine(inv + "->" + val);
}
}
}
}
//http://rosalind.info/problems/orf/
public OpenReadingFrames()
{
var proteins = new List <ProteinString>();
string input = FASTAToDictionary.Convert(File.ReadAllLines(@"C:\code\dataset.txt").ToList()).First().Value.Replace('T', 'U');
FindProteinOpenFrames(proteins, input);
FindProteinOpenFrames(proteins, input.Substring(1));
FindProteinOpenFrames(proteins, input.Substring(2));
input = ComplementingAStrandOfDna.ReverseCompliment(input, true);
FindProteinOpenFrames(proteins, input);
FindProteinOpenFrames(proteins, input.Substring(1));
FindProteinOpenFrames(proteins, input.Substring(2));
proteins.Select(p => p.Protein).Distinct().ToList().ForEach(p => Console.WriteLine(p));
}
//http://rosalind.info/problems/dbru/
public ConstructingADeBruijnGraph()
{
string[] inputList = File.ReadAllLines(@"C:\code\dataset.txt");
var dnaList = new List <string>(inputList);
foreach (var item in inputList)
{
dnaList.Add(ComplementingAStrandOfDna.ReverseCompliment(item, false));
}
dnaList = dnaList.Distinct().ToList();
foreach (var item in dnaList)
{
Console.WriteLine(string.Format("({0}, {1})", item.Substring(0, item.Length - 1), item.Substring(1, item.Length - 1)));
}
}
//http://rosalind.info/problems/revp/
public LocatingRestrictionSites()
{
string input = FASTAToDictionary.Convert(File.ReadAllLines(@"C:\code\dataset.txt").ToList()).First().Value;
string reversed = ComplementingAStrandOfDna.ReverseCompliment(input, false);
for (int i = 0; i < input.Length - 3; i++)
{
for (int j = 4; j <= 12; j++)
{
if (i + j > input.Length)
{
break;
}
if (input.Substring(i, j).Equals(reversed.Substring(input.Length - (i + j), j)))
{
Console.WriteLine(i + 1 + " " + j);
}
}
}
}
