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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.
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Inherited from Inherited from |
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alphabets =
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re_symbol = re.compile(r'\S
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x.__init__(...) initializes x; see x.__class__.__doc__ for signature
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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], } |
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alphabets
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