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$ perl -Mstrict -Mwarnings -e '
    my @fasta = (">dddd\n", "abcdef\n", ">eeee\n", "bcdef\n");
...
aaaaabcdef
>eeee
aaaabcdef

while (<$input_fh>) {
    print $output_fh 'aaaa' unless /^>/;
    print $output_fh $_;
}