my ($left_of_boundary, $intron_from_boundary, $new_left, $seq, $col7, $col_alt, $matchID);
my $i = 0;
open (INTRONS_five, '>fasta_introns_five_non');
open (INTRONS_three, '>fasta_introns_three_non');
foreach $col7(@col7) { ##50bp seq in var file
$seq = '';
$col7[$i] =~ s/\[[ACTG]\]/$col_ref[$i]/i;


		if ($intron_from_boundary[$i] =~ m/\-/) { 
		
			&three_prime;
		
		}
			elsif ($intron_from_boundary[$i] =~ m/\+/) {
					
				&five_prime;
			
			}
			

		my $length = length($seq);
		if ($length == 9) {
			print INTRONS_five (">" . "$match{$col_NM[$i]}" . "\n", lc($seq),"\n");	
}			
		elsif ($length != '') {
			print INTRONS_three (">" . "$col_NM[$i]" . "\n", lc($seq),"\n");	
}			
			
	++$i; 
	}
	close (INTRONS_five);
	close (INTRONS_three);
	
	
	
	
	sub three_prime {
	 
				if ($strands{$ID[$i]} =~ m/\+/) {
				
				## !!!PROBLEM!!! - $seq prints to file INTRONS_three 
when $strands{$ID[$i]} = + or - ###
				### BUT if I print out $ID[$i] here, it only pulls out
 + (shows the hash is working) ###
				
			$left_of_boundary = 20;
			##$right_of_boundary = 3;
	 
			$left_of_boundary = $left_of_boundary + $intron_from_boundary[$i]; 

			$new_left = 51 - $left_of_boundary; 
			
				$seq = substr( $col7[$i], $new_left, 23);

			}
			
			elsif ($strands{$ID[$i]} =~ m/\-/) {
			
			
			if ($intron_from_boundary[$i] >= -6) {
			$left_of_boundary = 3; 
			#$right_of_boundary = 6;
		
			$left_of_boundary = $left_of_boundary - $intron_from_boundary[$i]; 

			$new_left = 51 - $left_of_boundary; 
			
				$seq = substr( $col7[$i], $new_left, 9);
				$matchID = $ID[$i] . "\t" . $intron_from_boundary[$i] . "\t" . "on the negative strand";
				
			}
		}	
		}