Dearest Monks, I have been playing around with the same code for over a day and I still don't understand where I'm falling down. I'm trying to pull out a certain sequence based on certain conditions and then print to a file the results. Unfortunately, what ends up printing to file is multiple matches of the same sequence. I have done a few tests and have commented out what happens when I print out the sequence at different stages in my code. I have tried googling,using books,pure determination, and I'm still confused... Please can you help?

my ($value, $col, $col2, $l_o_b, $left, $matchedID, $diff_three_prime,
+ $diff_five_prime, $sequence);
open (EXONS_five, '>fasta_exons_five');
open (EXONS_three, '>fasta_exons_three');
my $i = 0;
foreach my $match(@exonic_matches) { 

$value = $exon_ID[$i];
$col = $exon_left{$value};
$col2 = $exon_right{$value};
my @three_prime_ss = split(",", $col);  
my @five_prime_ss = split(",", $col2); 
my @reverse_three = reverse(@three_prime_ss);
my @reverse_five = reverse(@five_prime_ss);


    if ($strands{$value} =~ m/\+/) {

    $diff_three_prime = $LBP[$i] - $three_prime_ss[$exons2{$value} - 1
+]; 
    $diff_five_prime = $LBP[$i] - $five_prime_ss[$exons2{$value} - 1];
+ 
    $matchedID = $ID{$LBP[$i]};
    
    if ($diff_three_prime !~ m/\-/ && $diff_three_prime <= 3) {
    
    $BP{$LBP[$i]} =~ s/\[[ACTG]\]/$alt[$i]/i; 
    
    $l_o_b = 20;
    ##$right_of_boundary = 3;
     
            $l_o_b = $l_o_b + $diff_three_prime; 

            $left = 51 - $l_o_b; 

    $sequence = substr($BP{$LBP[$i]}, $left, 23);
    ##    print $sequence, "\n"; 
## POINT ONE: prints out correct sequence for condition ##
    }
        
    elsif ($diff_five_prime =~ m/\-/ && $diff_five_prime >= -3) {
    
    $BP{$LBP[$i]} =~ s/\[[ACTG]\]/$alt[$i]/i; 
    
    $l_o_b = 3;
    ##$right_of_boundary = 6;
     
            $l_o_b = $l_o_b + $diff_five_prime; 

            $left = 51 - $l_o_b; 
    
    $sequence = substr( $BP{$LBP[$i]}, $left, 9);
    ##    print $sequence, "\n"; 
## POINT TWO: prints out what I want for this condition plus some repe
+ats ##
        }
 }

    
        ##    print $sequence, "\n"; 
## POINT THREE: prints out multiple sequences of the above ##
    my $seq_length = length($sequence);
    if ($seq_length == 9) {
    
    print EXONS_five (">" . "$match_exon{$matchedID}" . "\n", lc($sequ
+ence),"\n");    
    }
        else {
    print EXONS_three (">" . "$match_exon{$matchedID}" . "\n", lc($seq
+uence),"\n");
    }
$i++;
}
    close (EXONS_five);
    close (EXONS_three);

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In reply to looping foreach error by Anonymous Monk

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