Package obitools :: Package seqdb :: Package genbank :: Class GpepSequence
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Class GpepSequence

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Class used to represent a peptidic sequence issued from Genpep.

Instance Methods [hide private]
 
__init__(self, id, seq, de, header, featureTable, secondaryAcs, **info)
BioSequence constructor.
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__getGeneRef(self) source code
bool
geneAvailable(self)
Predicat indicating if reference to the nucleic sequence encoding this protein is available in feature table.
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NucBioSeq
getCDS(self, database)
Return the nucleic sequence coding for this protein if data are available.
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Inherited from AnnotatedSequence: extractTaxon, getFeatureTable, getHeader, getSecondaryAcs

Inherited from AASequence: isNucleotide

Inherited from BioSequence: __contains__, __delitem__, __getitem__, __iter__, __len__, __setitem__, __str__, getDefinition, getId, getRoot, getStr, getSubSeq, getSymbolAt, getTags, getWrappers, items, iteritems, iterkeys, 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]

Inherited from AnnotatedSequence: featureTable, header, secondaryAcs

Inherited from BioSequence: definition, id, wrappers

Inherited from object: __class__

Method Details [hide private]

__init__(self, id, seq, de, header, featureTable, secondaryAcs, **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)

geneAvailable(self)

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Predicat indicating if reference to the nucleic sequence encoding this protein is available in feature table.

Returns: bool
True if gene description is available

getCDS(self, database)

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Return the nucleic sequence coding for this protein if data are available.

Parameters:
  • database (a dict like object) - a database object where looking for the sequence
Returns: NucBioSeq
a NucBioseq instance carreponding to the CDS
Raises:
  • AssertionError - if no gene references are available

See Also: geneAvailable