Close handle in doctest
Simply doctests by using filenames for SeqIO
Simplify a doctest example using a filename with SeqIO
Fix use of deprecated assert_ method in RAXML test
Fix use of deprecated assert_ method in BGZF test
Close handles in test_geo.py
Close handles in test_Uniprot.py using context managers
Fix leaked handles in test_SeqUtils.py
Close handles in test_SubsMat.py using context managers
Fix handle leaks in test_TCoffee_tool.py by passing SeqIO filenames
Fix handle leaks in test_SeqIO_features.py
Replace deprecated assertEquals call with assertEqual
Fix another handle leak by using a context manager
Fix another handle leak by using a context manager
Ensure Astral FASTA handle is closed
Fix some more handle leaks
Fix more handle leaks in test_SeqIO_QualityIO.py
Fix unclosed handle in test_TogoWS.py
Missed another unclosed handle in test_SeqIO_features.py
Using context managers here is actually nicer I think.

Also it fixes two unclosed handles.