Hi monks, I'm feeling a bit stuck. I basically am writing a sub-routine that compares two strings of dna, and prints out any mismatches that occur ( where good base-pairs are defined in the sub). My problem is that if the mismatch occurs on the first or last base of the string it messes up. e.g. for a sequence:

ATCG
AAGG
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Mismatches are present on first and last positions e.g. A/A and G/G. I want the program to also print the bases either side of the mismatches e.g. AT/AA and CG/GG. But if the mismatch is on the first position it prints GA/GA and if it is on the last position it prints G/G. How can I get it to not print [$i -1] if the mismatch has occured on the first position, and to not print [$i+1] if the mismatch is on the last position. Thanks for your help. ;-)

sub get_mismatches   {

    my ($segment, $comp_segment) = @_;
    my @seg_mismatches;
    my @seg_mis;
    my $i;

    my %good_pairs = (
                      'A' => 'T',
                      'C' => 'G',
                      'G' => 'C',
                      'T' => 'A',
                      );



    foreach (my $i =0; $i < @$segment; $i++)       {


       if ($segment->[$i] ne $good_pairs {$comp_segment->[$i]})     {

             push @seg_mismatches,"$segment->[$i-1]$segment->[$i]/$com
+p_segment->[$i-1]$comp_segment->[$i]\n";


             push @seg_mismatches, "$segment->[$i]$segment->[$i+1]/$co
+mp_segment->[$i]$comp_segment->[$i+1]\n";
             push @seg_mis, "$segment->[$i-1]$segment->[$i] $segment->
+[$i]$segment->[$i+1]\n";

       }


  }


    return (\@seg_mismatches, \@seg_mis);

}
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update (broquaint): escaped square brackets + title change (was strings)

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