Hello ejbiers.

 print "###:".$hit->name . $hit->description."\n";
__DATA__
###:43989.cce_0262(Cyanothece ATCC 51142)
[download]

This is first time I looked into BioPerl. I have no idea for why name method stores it, just found it while looking around modules of bio perl.

Your XML lacks several end tags.
And real command line, I guess ,

perl scriptname.pl -i inputfile.xml -o goodoutputfile.txt -t test.txt -n 3 -b 1

I hope you fixing them and get more proper answers from bio perl monks.

regards.