Class Sequence

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

Parameters:

• type - type of sequence ('dna', 'rna', or 'protein').
• symbol - short symbol of the sequence, e.g. 'ACTM' (max. 10 chars)
• name - full name of the sequence, e.g. 'muscle Actin'
• location - location of a sequence on a genome/chromosome.
• annotations - list of Annotation objects
• domain_architecture - protein domains on this sequence (type DomainArchitecture)
• other - list of non-phyloXML elements (type Other)

Overrides: object.__init__

(inherited documentation)

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],
   }

alphabets

Value:

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