Package Bio :: Package GFF :: Module GenericTools
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Module GenericTools

source code

A set of generic bits of code under Bio.GFF (DEPRECATED).

This is part of the "old" Bio.GFF module by Michael Hoffman, which offered access to a MySQL database holding GFF data loaded by BioPerl. This code has now been deprecated, and will probably be removed in order to free the Bio.GFF namespace for a new GFF parser in Biopython (including GFF3 support).

Classes [hide private]
  AppendableListDictionary
a dictionary of lists
  ForgivingDictionary
  VerboseDict
  VerboseList
  TempFile
  SurrogateNotInitedError
  Surrogate
the data is stored in _data
  ArgsParser
Functions [hide private]
 
defline_text(defline) source code
 
is_nestable(x)
Returns 1 if x is a tuple or list (sequence types that can nest) Returns 0 otherwise
source code
 
dump_list(l)
returns strings of list
source code
 
reverse_text(text) source code
 
all(iterator) source code
 
_test()
Run the Bio.GFF.GenericTools module's doctests (PRIVATE).
source code
Function Details [hide private]

is_nestable(x)

source code 

Returns 1 if x is a tuple or list (sequence types that can nest) Returns 0 otherwise

>>> is_nestable("string")
0
>>> is_nestable((0,))
1
>>> is_nestable(range(5))
1

_test()

source code 

Run the Bio.GFF.GenericTools module's doctests (PRIVATE).

This will try and locate the unit tests directory, and run the doctests from there in order that the relative paths used in the examples work.