Each iteration of your while loop overwrites the variables $V1 and $V2, so by the time your while loop is complete, only the final line's values are there.

Something like this (untested) should work:

use Bio::SeqIO;

my (%all_V1, %all_V2); # hashes to store $V1 and $V2
open (LIST1, "list");
while (<LIST1>) {
    ($V1, $V2) = split /\t/;
    $all_V1{$V1}++; # FIX: this line and the next were originally
    $all_V2{$V2}++; #      incorrectly prefixed with "push".
}
close(LIST1);

my $seqIO_object = Bio::SeqIO->new(-file=>"infile.gb");
my $seq_object = $seqio_object ->next_seq;

for my $feat_object ($seq_object->get_SeqFeatures){
    if ($feat_object->primary_tag eq "CDS"){
        if ($feat_object->has_tag('locus_tag')){
            for my $V3 ($feat_object ->get_tag_values('locus_tag')){
                if (exists $all_V1{$V3}){
                    print "locus_tag: ", $V3, " is unique\n";
                }
            } 
         }
     }
}

[download]

By the way, $V1, $V2 and $V3 are very badly named variables. If you want to be able to come back to your code in a few months and fix a bug, it really helps if your variables have useful names.

In reply to Re: Question on loops by tobyink
in thread Question on loops by Bforde

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