Python deprecation warnings with 3.8

[smoe]

Hello, shout out if you prefer patches. The dendropy one is not your immediate business - anyway. Regards, Steffen

gubbins/python/gubbins/common.py:537: DeprecationWarning: invalid escape sequence \d
  elif re.match('^\d', vcf_line) is not None:
gubbins/python/gubbins/common.py:612: DeprecationWarning: invalid escape sequence \d
  search_obj = re.search('misc_feature    ([\d]+)..([\d]+)$', line)
gubbins/python/gubbins/common.py:619: DeprecationWarning: invalid escape sequence \=
  search_taxa = re.search('taxa\=\"([^"]+)\"', line)
/usr/lib/python3/dist-packages/dendropy/utility/container.py:357: DeprecationWarning: Using or importing the ABCs from 'collections' instead of from 'collections.abc' is deprecated since Python 3.3,and in 3.9 it will stop working
  class CaseInsensitiveDict(collections.MutableMapping):
/usr/lib/python3/dist-packages/Bio/Alphabet/__init__.py:26: PendingDeprecationWarning: We intend to remove or replace Bio.Alphabet in 2020, ideally avoid using it explicitly in your code. Please get in touch if you will be adversely affected by this. https://github.com/biopython/biopython/issues/2046
  PendingDeprecationWarning)

[puethe]

Hi Steffen, we don't really have resources for Gubbins maintenance at the moment, but if you provide a PR I'm more than happy to merge it in to get rid of these warnings. Thanks, Christoph