Hello all, I'm a new Bioinformatics grad student, and I'm pretty new to perl programming, so if my code looks C'ish, forgive me: In a perl script I'm coding, I 'think' I'm having trouble with variable scope, in this code I wrote (all this is actually in a while loop not posted): 
push( @next_cell_arr, $protein_matrix[$row][$col+1] );

        push( @next_cell_arr, $protein_matrix[$row+1][$col+1] );

        push( @next_cell_arr, $protein_matrix[$row+1][$col] );
    
        # - debug
        #$arr_len = scalar @next_cell_arr;
        #for( $var = 0; $var < $arr_len; $var++ ){
        #    print $next_cell_arr[$var];
        #    print "\n";
        #}
        #print "\n\n";
        #exit;
        # - debug
        
        # - if all values are equal, then the sequence gets a match of
+ suffers a mismatch (diagonal move), and not a gap penalty.  This als
+o saves me from having to compute the max of the three cells
        if( ($next_cell_arr[0] == $next_cell_arr[1]) && ($next_cell_ar
+r[1] == $next_cell_arr[2]) ){
                push( @sequence_2_arr, $protein_matrix[0][$col+1] );
                push( @sequence_1_arr, $protein_matrix[$row+1][0] );
                $dowhat = "diagonal";
        }

[download]
The debug code block in there lets me see the contents of the array I'm pushing data onto. I checked the contents in array, and they are loading correctly. The problem is in my bottom 'if' statement. When I try to utilize the values in the array within the 'if' statement, the Perl interpreter tells me: "Use of uninitialized value in numeric eq (==)," at this line. I'm not sure why, but this looks like I'm accessing the array out of scope. Does anyone know what's wrong?

In reply to Understanding variable scope in perl by BioBoy

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