open (INFILE, $ARGV[0]);  # open file

$Seq = "";    # initialize sequence

while (<INFILE>) {

  unless (/>/) {

    chomp;
    $Seq .= $_;    # NOTE:  assumes only one sequence

  }

}

$Len = length ($Seq);   # length of sequence
$End = $Len - 1;        # number of 2-mers in sequence

#loop over all 2-mers
for ($i = 0; $i < $End ; $i++) {

  $Sing = substr ($Seq, $i, 1);  # get single base
  $Two = substr ($Seq, $i, 2);   # get two bases

  $Freq{$Sing}++;      # increment counters
  $BiFreq{$Two}++;

}

#process last nucleotide
$Sing = substr ($Seq, $End, 1);
$Freq{$Sing}++;

# compute nucleotide frequencies
foreach $key (keys (%Freq)) {

  $Freq{$key} /= $Len;

}

# compute dinucleotide frequencies
foreach $key (keys (%BiFreq)) {

  $BiFreq{$key} /= $End;

}

open (QFILE, $ARGV[1]);    # open query sequence file

$Query = "";    # initialize sequence

while (<QFILE>) {
  
  unless (/>/) {

    chomp;
    $Query .= $_;

  }

}

# get first nucleotide and initialize based on multinomial model
$Sing = substr ($Query, 0, 1);
$Ans = log ($Freq{$Sing});

# calculate number of 2-mers
$End = length ($Query)  - 1;

# calculate 1-order model based on two-mer representation
for ($i = 0; $i < $End; $i++) {
  
   $Two = substr ($Query, $i, 2);
   $Ans += log ($BiFreq{$Two});    # NOTE:  log = natural log in perl

 }

print "Log probability:  $Ans\n";  # answer