autopep8 --in-place --select E305 Bio/*.py

Author: peterjc

Bio/DocSQL.py

@@ -225,6 +225,7 @@ def _test(*args, **keywds):
  import doctest
  doctest.testmod(sys.modules[__name__], *args, **keywds)
 
+
 if __name__ == "__main__":
  if __debug__:
  _test()

Bio/Index.py

@@ -143,4 +143,5 @@ def _toobj(self, str):
  intlist = array.array('b', intlist)
  return pickle.loads(''.join(chr(i) for i in intlist))
 
+
 Index = _InMemoryIndex

Bio/MarkovModel.py

@@ -50,6 +50,7 @@ def itemindex(values):
  d[key] = n - index
  return d
 
+
 numpy.random.seed()
 
 VERY_SMALL_NUMBER = 1E-300
@@ -198,6 +199,7 @@ def train_bw(states, alphabet, training_data,
  p_initial, p_transition, p_emission = x
  return MarkovModel(states, alphabet, p_initial, p_transition, p_emission)
 
+
 MAX_ITERATIONS = 1000
 
 

Bio/MaxEntropy.py

@@ -316,6 +316,7 @@ class assignments for each observation.  feature_fns is a list of
 
  return me
 
+
 if __name__ == "__main__":
  from Bio._utils import run_doctest
  run_doctest(verbose=0)

Bio/Seq.py

@@ -56,6 +56,7 @@ def _maketrans(complement_mapping):
  else:
  return string.maketrans(before, after)
 
+
 _dna_complement_table = _maketrans(ambiguous_dna_complement)
 _rna_complement_table = _maketrans(ambiguous_rna_complement)
 
@@ -2276,5 +2277,6 @@ def _test():
  doctest.testmod(optionflags=doctest.IGNORE_EXCEPTION_DETAIL)
  print("Done")
 
+
 if __name__ == "__main__":
  _test()

Bio/_utils.py

@@ -116,5 +116,6 @@ def run_doctest(target_dir=None, *args, **kwargs):
  os.chdir(cur_dir)
  print("Done")
 
+
 if __name__ == "__main__":
  run_doctest()

Bio/triefind.py

@@ -71,6 +71,7 @@ def find(string, trie):
  start += 1
  return results
 
+
 DEFAULT_BOUNDARY_CHARS = string.punctuation + string.whitespace