use strict;
use warnings;

local $/;
my ($name, $aa);

while (my $seq = <DATA>) {
    if ($seq =~ />(\w+).+aa\)\n(\w+)/m) {
        $name = $1;
        $aa = $';
    }
}

print "$name $aa\n";
__DATA__
>CIMG_12545 | Coccidioides immitis RS hypothetical protein (translation) (95 aa)
MSSQPTTLQSQTGIQRHGEISSQAQKPTTALEEDDEFEDFPVEDWPQEDAEALGPAGTNN
DHLWEESWDDDDSNEEFSRQLKEELKKVEAMKQQ*