Package Bio :: Package Phylo :: Module PhyloXML :: Class Sequence
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Class Sequence

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          object --+        
                   |        
BaseTree.TreeElement --+    
                       |    
            PhyloElement --+
                           |
                          Sequence

A molecular sequence (Protein, DNA, RNA) associated with a node.

One intended use for id_ref is to link a sequence to a taxonomy (via the taxonomy's id_source) in case of multiple sequences and taxonomies per node.

Instance Methods [hide private]
 
__init__(self, type=None, id_ref=None, id_source=None, symbol=None, accession=None, name=None, location=None, mol_seq=None, uri=None, domain_architecture=None, annotations=None, other=None)
x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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to_seqrecord(self)
Create a SeqRecord object from this Sequence instance.
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get_alphabet(self) source code

Inherited from BaseTree.TreeElement: __repr__, __str__

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

Class Methods [hide private]
 
from_seqrecord(cls, record, is_aligned=None)
Create a new PhyloXML Sequence from a SeqRecord object.
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Class Variables [hide private]
  alphabets = {'dna': DNAAlphabet(), 'protein': ProteinAlphabet(...
  re_symbol = re.compile(r'\S{1,10}')
Properties [hide private]

Inherited from object: __class__

Method Details [hide private]

__init__(self, type=None, id_ref=None, id_source=None, symbol=None, accession=None, name=None, location=None, mol_seq=None, uri=None, domain_architecture=None, annotations=None, other=None)
(Constructor)

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

Parameters:
  • type ({'dna', 'rna', 'protein'}) - type of molecule this sequence represents
  • id_ref (string) - reference to another resource
  • id_source (string) - source for the reference
  • symbol (string) - short symbol of the sequence, e.g. 'ACTM' (max. 10 chars)
  • accession (Accession) - accession code for this sequence.
  • name (string) - full name of the sequence, e.g. 'muscle Actin'
  • location - location of a sequence on a genome/chromosome.
  • mol_seq (MolSeq) - the molecular sequence itself
  • uri (Uri) - link
  • annotations (list of Annotation objects) - annotations on this sequence
  • domain_architecture (DomainArchitecture) - protein domains on this sequence
  • other (list of Other objects) - non-phyloXML elements
Overrides: object.__init__
(inherited documentation)

to_seqrecord(self)

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Create a SeqRecord object from this Sequence instance.

The seqrecord.annotations dictionary is packed like so:

{ # Sequence attributes with no SeqRecord equivalent:
  'id_ref': self.id_ref,
  'id_source': self.id_source,
  'location': self.location,
  'uri': { 'value': self.uri.value,
                  'desc': self.uri.desc,
                  'type': self.uri.type },
  # Sequence.annotations attribute (list of Annotations)
  'annotations': [{'ref': ann.ref,
                   'source': ann.source,
                   'evidence': ann.evidence,
                   'type': ann.type,
                   'confidence': [ann.confidence.value,
                                  ann.confidence.type],
                   'properties': [{'value': prop.value,
                                    'ref': prop.ref,
                                    'applies_to': prop.applies_to,
                                    'datatype': prop.datatype,
                                    'unit': prop.unit,
                                    'id_ref': prop.id_ref}
                                   for prop in ann.properties],
                  } for ann in self.annotations],
}

Class Variable Details [hide private]

alphabets

Value:
{'dna': DNAAlphabet(),
 'protein': ProteinAlphabet(),
 'rna': RNAAlphabet()}