#!/usr/bin/perl -w

use strict;
use warnings;

use Getopt::Long qw( GetOptions );

# Get user input.
my $abstracts_file;
my $terms_file;
GetOptions(
   "pathway_abstracts=s" => \$abstracts_file,
   "terms_file=s"        => \$terms_file,
);
# ...Needs error checking here...

# Load pathway abstract.
my $file;
{
  open(my $fh, '<', $abstracts_file)
    or die("Unable to open abstracts file \"$abstracts_file\": $!\n");
  local $/;
  $file = <$fh>;
}

# Load terms into array.
my @terms;
{
  open(my $fh, '<', $terms_file)
    or die("Unable to open terms file \"$terms_file\": $!\n");
  chomp( @terms = <$fh> );
}

print("Term\t| ");
print("Number\t| ");
print("Frequency\n");
print("----------------------------------------------------\n");

# Find out how many words are in abstracts.
my $word_count = () = split(' ', $file);

for my $term (@terms) {
  # Count the number of times the search term matches.
  my $score = () = $file =~ /\b\Q$term\E\b/g;
  my $freq = $score / $word_count;
  print("$term\t$score\t$freq\n");
}