/* 

  Rosalind problem Consensus and Profile in Picat.

  https://rosalind.info/problems/cons/
  """
  Problem
  A matrix is a rectangular table of values divided into rows and columns. An m×n matrix has m rows 
  and n columns. Given a matrix A, we write Ai,j to indicate the value found at the intersection 
  of row i and column j.

  Say that we have a collection of DNA strings, all having the same length n. Their profile matrix 
  is a 4×n matrix P in which P1,j represents the number of times that 'A' occurs in the jth position 
  of one of the strings, P2,j represents the number of times that C occurs in the jth position, 
  and so on (see below).

  A consensus string c is a string of length n formed from our collection by taking the most common 
  symbol at each position; the jth symbol of c therefore corresponds to the symbol having the maximum 
  value in the j-th column of the profile matrix. Of course, there may be more than one most common symbol, 
  leading to multiple possible consensus strings.

  DNA Strings
  A T C C A G C T
  G G G C A A C T
  A T G G A T C T
  A A G C A A C C
  T T G G A A C T
  A T G C C A T T
  A T G G C A C T

  Profile	
  A   5 1 0 0 5 5 0 0
  C   0 0 1 4 2 0 6 1
  G   1 1 6 3 0 1 0 0
  T   1 5 0 0 0 1 1 6

  Consensus	
      A T G C A A C T

  Given: A collection of at most 10 DNA strings of equal length (at most 1 kbp) in FASTA format.

  Return: A consensus string and profile matrix for the collection. (If several possible consensus strings 
  exist, then you may return any one of them.)

  Sample Dataset
     >Rosalind_1
     ATCCAGCT
     >Rosalind_2
     GGGCAACT
     >Rosalind_3
     ATGGATCT
     >Rosalind_4
     AAGCAACC
     >Rosalind_5
     TTGGAACT
     >Rosalind_6
     ATGCCATT
     >Rosalind_7
     ATGGCACT
  Sample Output
    ATGCAACT
    A: 5 1 0 0 5 5 0 0
    C: 0 0 1 4 2 0 6 1
    G: 1 1 6 3 0 1 0 0
    T: 1 5 0 0 0 1 1 6
  """


  This model was created by Hakan Kjellerstrand, hakank@gmail.com
  See also my Picat page: http://www.hakank.org/picat/

*/

import util.
import rosalind_utils.

main => go.

go ?=>
  File = "rosalind_cons_fasta1.txt",
  % File = "rosalind_cons_fasta_challenge.txt",

  S = read_file_chars(File),

  Fs = [F[2] : F in  parse_fasta(S)],
  Map = new_map([1='A',2='C',3='G',4='T']),
  % This is in rosalind_utils.pi
  consensus_and_profile(Fs,Map, Consensus,Profile),

  % Result
  println(Consensus.to_list),
  foreach(I in 1..4)
    printf("%w: %w\n", Map.get(I), [P.to_string : P in Profile[I]].join(" "))
  end,
  
  nl.
go => true.