#!usr/bin/perl
use DBI;
use Data::Dumper;
use strict; use warnings;
use CGI;




my $filename = $ARGV[0];

my $tablename = $ARGV[1];
my $outfile = $ARGV[2];
open(INPUT, $filename);


my $line;
my $i;
my $sth;
while ($line = <INPUT>)
{
	
	# Get the block identifier
	my $blockID;
	$line = <INPUT>;
	chomp($line);
	$blockID = $line;
	$i++;
	#print "\n"."New block: $blockID"."\n";
	
	# Skip the next four lines
	<INPUT>;
	<INPUT>;
	<INPUT>;
	<INPUT>;

	open (MYOUTFILE, ">>./tmp/$outfile");
	while ($line = <INPUT>)
	
	{
		chomp($line);
		if (! $line)
		{
			last;
		}
		else
		{
			my $tmp = index($line, '#');
			
			if ($tmp == -1) # alignment lines
			{
				if (index($line, '*') == -1)
				{
					#print "$line\n";
				}
			}
			
			if ($tmp == 0) # genomic positions
			{
				#print "$line\n";
				my @fields = split('\t', $line);
				my $tmp = $fields[1];
				@fields = split(':', $tmp);
				my $chrom = $fields[1];
				my $start = $fields[2];
				my $stop = $fields[3];
			
				#print "$i\t\$blockID\n";
				#print "$i\t$line\t$chrom\t$start\t$stop\t$blockID\n";
				print MYOUTFILE"$i\t$start\t$stop\t$chrom\t$blockID\n";
				
			}
		}
	}

}
close (MYOUTFILE);



close (INPUT);