Long long ago on usenet, Tom Christiansen once wrote: If you find yourself calling cat with just one argument, you're probably doing something silly. So you should lose the cat and replace:

cat file.txt | perl -ne '...' > fastafile.fa
[download]

with:

perl -ne '...' file.txt > fastafile.fa
[download]

Update: See also Re: perl one liner for csv file one field (useless use of cat and other awards References)