Initial stab at reading from files.

This version reads from STDIN, so to read from a file you'll need to
redirect a file to stdin with the < operator. (e.g. fasta < file)

I also added a -q (quiet) argument; that stops it from spitting out the
variable prompts when running from a file.
Merge pull request #2 from xandrasings/read-from-file

Initial stab at reading from files.