Package obitools :: Package ecopcr :: Module taxonomy :: Class Taxonomy
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Class Taxonomy

source code


Instance Methods [hide private]
 
__init__(self)
The taxonomy database constructor
source code
 
findTaxonByTaxid(self, taxid) source code
 
findTaxonByName(self, name) source code
 
findRankByName(self, rank) source code
 
findIndex(self, taxid) source code
 
subTreeIterator(self, taxid)
return subtree for given taxonomic id
source code
 
parentalTreeIterator(self, taxid)
return parental tree for given taxonomic id starting from first ancester to the root.
source code
 
isAncestor(self, parent, taxid) source code
 
lastCommonTaxon(self, *taxids) source code
 
getScientificName(self, taxid) source code
 
getRankId(self, taxid) source code
 
getRank(self, taxid) source code
 
getTaxonAtRank(self, taxid, rankid) source code
 
getSpecies(self, taxid) source code
 
getGenus(self, taxid) source code
 
getFamily(self, taxid) source code
 
getOrder(self, taxid) source code
 
rankIterator(self) source code

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

Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self)
(Constructor)

source code 

The taxonomy database constructor

Parameters:
  • path (str) - path to the ecoPCR database including the database prefix name
Overrides: object.__init__