#!usr/bin/perl 
use strict;
use library;

### Only works for palindromic RE sites ###

# read in DNA sequence. #
my $filename = usrquery ("Please enter filename\n");
my @filedata = read_file_data ($filename);
my $sequence = extract_sequence (@filedata);
my $tag = extract_tag (@filedata);
$sequence =~ tr/actg/ACTG/;

# Create REBASE hash #
my $REfile = 'REBASE';
my %rebase_hash = parseREBASE ($REfile);

my $site = '';
my $regexp = '';

print "\nPlease enter filename for outfile.\n\n";
my $outputfile = <STDIN>;
chomp $outputfile;
unless 	(open(OUTFILE, ">$outputfile"))
	{print "Cannot open file \"OUTFILE\" to write to";
	exit;}
print OUTFILE "$tag\n\n######################################\n\n";

do 	{print "\n\nPlease enter a RE name (CASE-SENSITIVE) or press spacebar (quit).\n\n";
	my $query = <STDIN>;
	chomp $query;
	if ($query =~ /^\s*$/)
		{exit;}
	else 	{if (exists $rebase_hash{$query}) 
			{($site, $regexp) = split (" ", $rebase_hash{$query});
			print OUTFILE "$query";
			print "\n$site\n";
			print OUTFILE "\n$site";
			}else	{print "\n$query not found in database.\n";
				print OUTFILE "$query not found in database.\n";
				exit;}
		}
	my @matches = match_positions ($regexp, $sequence);
	if (@matches)
		{print "\nSites found at positions: @matches.";
		print OUTFILE "\nSites found at positions: \n\n@matches.\n\n######################################\n\n";
		}else 	{print "\nNo sites found.";
			print OUTFILE "\nNo sites found.\n\n######################################\n\n";
			}
	}
until (my $query =~ /quit/ );

close (OUTFILE);

exit;