I am working with existing code, and trying to add a "filter" to it. Currently the code pulls an id number and a sequence from a table in the database.(sql1) A foreach loop then permutes each sequence and searches the list to find out if any of the alternates exists. This leads to way more matches than I need because the loop eventually gets to the existing alternates, permutes them, and finds all of the matches again, just with a different primary sequence. I created a second database pull that creates another list with the same id-sequence layout that contains only the primary keys that I want to evaluate. (sql2) I want to use this secondary list as the filter for which sequences are evaluated from the primary list, but I need each key identified in the secondary list to be evaluated against all of the primary list. 

#currently have strict turned off
#code snippet

foreach my $sql1 (@{$sql1}) {
    $table1{$sql1->[1]}{$sql1->[0]}=undef;  #rearranges the sql pull
}

foreach my $sql2 (@{$sql2}) {                
    $table2{$sql2->[1]}{$sql2->[0]}=undef;  #rearranges the sql pull
}

my %hash = ();
my @array = ();
my @bases = ('A','C','G','T');


foreach my $tar1 (keys %table1){        

    foreach my $tar2 (keys %table2) {

        if ($tar1 eq $tar2) {     

#a bunch of follow on code that works if the second foreach and if sta
+tements are removed

[download]

I'm just not sure which direction I should go with trying to limit the list it chooses to evaluate, without limiting the list of sequences it uses to evaluate against. I have tried several combinations of foreach/if/where statements and the closest I have gotten lead me to loop through the entire first table, but only using one sequence from the second table. I couldn't get it to iterate through the "filter" table. I'm sure my explanation is lacking severely.

In reply to Nested loops? by Speed_Freak

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