Use context manager for warnings filter in PDB
Use context manager for test_SeqIO_PdbIO.py warnings filters
Avoid deprecated BioSQL method
Move code from deprecated method into replacement.

This should have been done when adding the deprecation warning.
As it was, even using the new style delete the warning was still
being triggered.
Use context manager for warnings filter in BioSQL tests
Use context manager for test_GenBank.py warnings filter
Use context manager for warning filters in test_SeqIO.py
Context manager to silence deprecation warning for Bio.Motif tests
Avoid deprecated Seq's .tostring() in deprecate Bio.Motif code
Avoid deprecated Seq .tostring() method in deprecated test_Motif.py