Package obitools :: Class WrappedBioSequence
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Class WrappedBioSequence

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Instance Methods [hide private]
 
__init__(self, reference, id=None, definition=None, **info)
BioSequence constructor.
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getWrapped(self) source code
str
getDefinition(self)
Sequence definition getter
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getId(self) source code
 
isNucleotide(self) source code
 
iterkeys(self) source code
 
iteritems(self) source code
 
__getitem__(self, key) source code
str
getSymbolAt(self, position)
Return the symbole at position in the sequence
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posInWrapped(self, position, reference=None) source code
str
getStr(self)
Return the sequence as a string
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getRoot(self) source code
 
_posInWrapped(self, position) source code

Inherited from BioSequence: __contains__, __delitem__, __iter__, __len__, __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__

Properties [hide private]
  definition
Sequence Definition
  id
Sequence Identifier
  wrapped
Wrapped's Docstring

Inherited from BioSequence: wrappers

Inherited from object: __class__

Method Details [hide private]

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

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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)

getDefinition(self)

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Sequence definition getter

Returns: str
the sequence definition
Overrides: BioSequence.getDefinition
(inherited documentation)

getId(self)

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Overrides: BioSequence.getId

iterkeys(self)

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Overrides: BioSequence.iterkeys

iteritems(self)

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Overrides: BioSequence.iteritems

__getitem__(self, key)
(Indexing operator)

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Overrides: BioSequence.__getitem__

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)

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)

getRoot(self)

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Overrides: BioSequence.getRoot

Property Details [hide private]

definition

Sequence Definition

Get Method:
getDefinition(self) - Sequence definition getter
Set Method:
unreachable.setDefinition(self, value)

id

Sequence Identifier

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

wrapped

Wrapped's Docstring

Get Method:
getWrapped(self)