Package Bio :: Package Phylo :: Module PhyloXML :: Class Taxonomy
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Class Taxonomy

source code

          object --+        
                   |        
BaseTree.TreeElement --+    
                       |    
            PhyloElement --+
                           |
                          Taxonomy

Describe taxonomic information for a clade.
Instance Methods [hide private]
 
__init__(self, id_source=None, id=None, code=None, scientific_name=None, authority=None, rank=None, uri=None, common_names=None, synonyms=None, other=None)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
source code
 
__str__(self)
Show the class name and an identifying attribute.
source code

Inherited from BaseTree.TreeElement: __repr__

Inherited from object: __delattr__, __format__, __getattribute__, __hash__, __new__, __reduce__, __reduce_ex__, __setattr__, __sizeof__, __subclasshook__

Class Variables [hide private]
  re_code = re.compile(r'[a-zA-Z0-9_]{2,10}')
  ok_rank = set(['branch', 'class', 'cohort', 'cultivar', 'divis...
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, id_source=None, id=None, code=None, scientific_name=None, authority=None, rank=None, uri=None, common_names=None, synonyms=None, other=None)
(Constructor)

source code 
x.__init__(...) initializes x; see x.__class__.__doc__ for signature

Parameters:
  • id_source (Id) - link other elements to a taxonomy (on the XML level)
  • id (Id) - unique identifier of a taxon, e.g. Id('6500', provider='ncbi_taxonomy') for the California sea hare
  • code (restricted string) - store UniProt/Swiss-Prot style organism codes, e.g. 'APLCA' for the California sea hare 'Aplysia californica'
  • scientific_name (string) - the standard scientific name for this organism, e.g. 'Aplysia californica' for the California sea hare
  • authority (string) - keep the authority, such as 'J. G. Cooper, 1863', associated with the 'scientific_name'
  • common_names (list of strings) - common names for this organism
  • synonyms (list of strings) - synonyms for this taxon?
  • rank (restricted string) - taxonomic rank
  • uri (Uri) - link
  • other (list of Other objects) - non-phyloXML elements
Overrides: object.__init__
(inherited documentation)

__str__(self)
(Informal representation operator)

source code 
Show the class name and an identifying attribute.
Overrides: object.__str__

Class Variable Details [hide private]

ok_rank

Value:
set(['branch',
     'class',
     'cohort',
     'cultivar',
     'division',
     'domain',
     'family',
     'form',
...