Package obitools :: Class DNAComplementSequence
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Class DNAComplementSequence

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Instance Methods [hide private]
 
__init__(self, reference, id=None, definition=None, **info)
BioSequence constructor.
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getId(self) source code
 
__len__(self) source code
str
getStr(self)
Return the sequence as a string
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__iter__(self)
Iterate through the sequence symbols
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_posInWrapped(self, position) source code
str
getSymbolAt(self, position)
Return the symbole at position in the sequence
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complement(self) source code

Inherited from WrappedBioSequence: __getitem__, getDefinition, getRoot, getWrapped, isNucleotide, iteritems, iterkeys, posInWrapped

Inherited from BioSequence: __contains__, __delitem__, __setitem__, __str__, extractTaxon, getSubSeq, getTags, getWrappers, items, keys, register, setDefinition, setId

Inherited from BioSequence (private): _unregister

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

Class Variables [hide private]
  _comp = {'-': '-', 'a': 't', 'b': 'v', 'c': 'g', 'd': 'h', 'g'...
Properties [hide private]
  id
Sequence Identifier

Inherited from WrappedBioSequence: definition, wrapped

Inherited from BioSequence: wrappers

Inherited from object: __class__

Method Details [hide private]

__init__(self, reference, id=None, definition=None, **info)
(Constructor)

source code 

BioSequence constructor.

Parameters:
  • id - sequence identifier
  • seq - the sequence
  • definition - sequence definition (optional)
  • info - extra named parameters can be add to associate complementary data to the sequence
Overrides: object.__init__
(inherited documentation)

getId(self)

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Overrides: BioSequence.getId

__len__(self)
(Length operator)

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Overrides: BioSequence.__len__

getStr(self)

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Return the sequence as a string

Returns: str
the string representation of the sequence
Overrides: BioSequence.getStr
(inherited documentation)

__iter__(self)

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Iterate through the sequence symbols

Overrides: BioSequence.__iter__
(inherited documentation)

_posInWrapped(self, position)

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Overrides: WrappedBioSequence._posInWrapped

getSymbolAt(self, position)

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Return the symbole at position in the sequence

Parameters:
  • position - the desired position. Position start from 0 if position is < 0 then they are considered to reference the end of the sequence.
Returns: str
a one letter string
Overrides: BioSequence.getSymbolAt
(inherited documentation)

Class Variable Details [hide private]

_comp

Value:
{'-': '-',
 'a': 't',
 'b': 'v',
 'c': 'g',
 'd': 'h',
 'g': 'c',
 'h': 'd',
 'k': 'm',
...

Property Details [hide private]

id

Sequence Identifier

Get Method:
getId(self)
Set Method:
unreachable.setId(self, value)