while (<INFILE>){
    chomp;
    my $line = $_;
    my $headerHash;
    ...
    if ($line =~ /^>/){
        my $header = $line;
        if ($header =~ /(>gi.*)\[(.+)\](>gi.*)\[(.+)\]/){
            $headerHash{$1} = $2;
        }
        else{
            my $seq = $line;
            print OUTFILE $headerHash, "\n", $seq, "\n";
        }
    }
}