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my @fasta_objs =();
...
push @fasta_objs,$seqFile1->seq;
...
$fasta->write_seq($seqFile2) if (grep {$_ eq $seqFile2->seq} @fasta_ob
+js);

my %fasta_objs =();
...
++$fasta_objs{$seqFile1->seq};
...
$fasta->write_seq($seqFile2) if exists $fasta_objs{$seqFile2->seq};

++$fasta_objs{$seqFile1->seq};

$fasta_objs{$seqFile1->seq} = $header;

seq => [header1, header2, ...]

# Comment explaining why you're doing this
no strict 'refs';
... small piece of code here ...
use strict 'refs';