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

Class Sequence

          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.

: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

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

source code

to_seqrecord(self)
Create a SeqRecord object from this Sequence instance.

source code

get_alphabet(self)

source code

Inherited from BaseTree.TreeElement: __repr__, __str__

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

Class Methods

[hide private]

from_seqrecord(cls, record, is_aligned=None)
Create a new PhyloXML Sequence from a SeqRecord object.

source code

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)

source code

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

Overrides: object.__init__: (inherited documentation)

to_seqrecord(self)

source code

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()}

Class Sequence

__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)

to_seqrecord(self)

alphabets

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)