Hi again, I'm back.. much further in my program - but stuck again - 8 hours of solid playing around and still nothing.

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 + $intron_from_bound
+ary[$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 - $intron_from_bound
+ary[$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";
                
            }
        }    
        }

[download]

I know this is a lot of code (and not all of it), but I have commented out "problem" where the issue lies. My %strands works, but when I open the INTRONS_three file it is printing out sequences for both when $ID[$i] is + or -. I thought maybe it was to do with when I am calling my variables i.e. my $seq? I've tried using/not using a subroutine, data::dumping, hitting the keyboard, prayer.. but still to no avail...

In reply to error calling variables? Going insane... by lecb

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