biopython v1.71.0 Bio.Phylo.PhyloXML.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

Link to this section Summary

Functions

__init__()

Initialize value for a Sequence object

clean_dict()

Remove None-valued items from a dictionary

from_seqrecord()

Create a new PhyloXML Sequence from a SeqRecord object

to_seqrecord()

Create a SeqRecord object from this Sequence instance

Link to this section Functions

__init__()

Initialize value for a Sequence object.

clean_dict()

Remove None-valued items from a dictionary.

from_seqrecord()

Create a new PhyloXML Sequence from a SeqRecord object.

to_seqrecord()

Create a SeqRecord object from this Sequence instance.

The seqrecord.annotations dictionary is packed like so::

{ 
  '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 },

  '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],
}