[BioPython] Deprecated Bio.sequtils

[Brad Chapman]

Hello everyone;
In checking into a bug report, I suddenly realized for the first
time that Bio/sequtils.py and Bio/SeqUtils/__init__.py duplicate the
same code. It looks like sequtils.py was expanded to an entire
directory at some point but the duplication was never removed. Even
worse, there have been different fixes and additions to both parts.

To fix this problem, I've merged all the changes into
Bio/SeqUtils/__init__.py and officially deprecated Bio/sequtils.py.
The SeqUtils directory contains other useful manipulation code so
this seems the right way to do things without being too confusing.

For now Bio/sequtils.py raises a DeprecationWarning when used, but
still works (by importing the code from Bio/SeqUtils.py into it's
namespace. This will give people time to update their scripts
without breaking anything. To fix Scripts that reference
Bio/sequtils.py you need to change:

from Bio.sequtils import whatever

to:

from Bio.SeqUtils import whatever

Sorry about any difficulties this may cause. Bio/sequtils.py will
remain around for a while to maintain back compatibility with the
warning. Please let me know if I've done anything which does not
leave it back compatible.

Thanks!
Brad