Package Bio :: Package motifs :: Module matrix :: Class GenericPositionMatrix
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Class GenericPositionMatrix

source code

object --+    
         |    
      dict --+
             |
            GenericPositionMatrix
Known Subclasses:

Instance Methods [hide private]
new empty dictionary

__init__(self, alphabet, values)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
source code
 
__str__(self)
str(x)
source code
 
__getitem__(self, key)
x[y]
source code
 
reverse_complement(self) source code

Inherited from dict: __cmp__, __contains__, __delitem__, __eq__, __ge__, __getattribute__, __gt__, __iter__, __le__, __len__, __lt__, __ne__, __new__, __repr__, __setitem__, __sizeof__, clear, copy, fromkeys, get, has_key, items, iteritems, iterkeys, itervalues, keys, pop, popitem, setdefault, update, values

Inherited from object: __delattr__, __format__, __reduce__, __reduce_ex__, __setattr__, __subclasshook__

Class Variables [hide private]

Inherited from dict: __hash__

Properties [hide private]
  consensus
Returns the consensus sequence.
  anticonsensus
  degenerate_consensus
  gc_content
Compute the fraction GC content.

Inherited from object: __class__

Method Details [hide private]

__init__(self, alphabet, values)
(Constructor)

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

Returns:
new empty dictionary

Overrides: object.__init__
(inherited documentation)

__str__(self)
(Informal representation operator)

source code 
str(x)

Overrides: object.__str__
(inherited documentation)

__getitem__(self, key)
(Indexing operator)

source code 
x[y]

Overrides: dict.__getitem__
(inherited documentation)

Property Details [hide private]

consensus

Returns the consensus sequence.

Get Method:
unreachable.consensus(self) - Returns the consensus sequence.

anticonsensus

Get Method:
unreachable.anticonsensus(self)

degenerate_consensus

Get Method:
unreachable.degenerate_consensus(self)

gc_content

Compute the fraction GC content.

Get Method:
unreachable.gc_content(self) - Compute the fraction GC content.