using System.Collections.Generic;
using System.IO;
using System.Linq;

namespace BioHelper
{
    class Program
    {
        static List<(string, string)> ReadFasta(string fileName)
        {
            var fileLines = File.ReadAllLines(fileName);
            var output = new List<(string, string)>();
            string curContent = "";
            string curName = "";
            foreach (var line in fileLines)
            {
                if (line.Contains(">"))
                {
                    if (curContent != "")
                    {
                        output.Add((curName, curContent));
                    }
                    curName = line;
                    curContent = "";
                }
                else
                {
                    curContent += line;
                }
            }
            return output;
        }

        static void Main(string[] args)
        {
            var proteins = ReadFasta("augustus.whole_downloaded.aa");
            var queries = ReadFasta("dna_associated_proteins.fasta");
            List<string> result = new List<string>();
            foreach(var protein in proteins)
            {
                if (queries.Any(x => protein.Item2.Contains(x.Item2)))
                {
                    result.Add(protein.Item2);
                }
            }
            File.WriteAllLines("result.txt", result);
        }
    }
}