Convert code to Python 3 and minor improvements

Hi Stephen!

This PR does the following modifications:

Code was ported from Python 2 to Python 3 as Python 2 was officially retired in January 2020.
The error message Use the flag --db to specify a database was altered to Use the flag -d to specify a database to match the correct argument name.
The FASTA files are now read with Biopython, making parser much faster.
GC content is now computed with Biopython.
The requirement of specifying a database with -d was removed for gc-content and tetra-freq, since those modules don't use the database.
The code was formated with Black to keep formatting consistent.

snayfach / MAGpurify