Package Bio :: Package motifs :: Package jaspar :: Class Motif
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Class Motif

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object --+    
         |    
     Motif --+
             |
            Motif

A subclass of Bio.motifs.Motif used to represent a JASPAR profile.

Additional metadata information are stored if available. The metadata
availability depends on the source of the JASPAR motif (a 'pfm' format
file, a 'jaspar' format file or a JASPAR database).

Instance Methods [hide private]
 
__init__(self, matrix_id, name, alphabet=IUPACUnambiguousDNA(), instances=None, counts=None, collection=None, tf_class=None, tf_family=None, species=None, tax_group=None, acc=None, data_type=None, medline=None, pazar_id=None, comment=None)
Construct a JASPAR Motif instance.
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__str__(self)
Return a string represention of the JASPAR profile.
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__hash__(self)
Return the hash key corresponding to the JASPAR profile.
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__eq__(self, other) source code

Inherited from Motif: __len__, format, reverse_complement, weblogo

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

Properties [hide private]
  base_id
Return the JASPAR base matrix ID.
  version
Return the JASPAR matrix version.

Inherited from Motif: anticonsensus, background, consensus, degenerate_consensus, mask, pseudocounts, pssm, pwm

Inherited from object: __class__

Method Details [hide private]

__init__(self, matrix_id, name, alphabet=IUPACUnambiguousDNA(), instances=None, counts=None, collection=None, tf_class=None, tf_family=None, species=None, tax_group=None, acc=None, data_type=None, medline=None, pazar_id=None, comment=None)
(Constructor)

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Construct a JASPAR Motif instance.

Overrides: object.__init__

__str__(self)
(Informal representation operator)

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Return a string represention of the JASPAR profile.

We choose to provide only the filled metadata information.

Overrides: object.__str__

__hash__(self)
(Hashing function)

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Return the hash key corresponding to the JASPAR profile.

:note: We assume the unicity of matrix IDs

Overrides: object.__hash__

Property Details [hide private]

base_id

Return the JASPAR base matrix ID.

Get Method:
unreachable.base_id(self) - Return the JASPAR base matrix ID.

version

Return the JASPAR matrix version.

Get Method:
unreachable.version(self) - Return the JASPAR matrix version.