sbol_utilities.workarounds
Module Contents
Functions
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Find the parent of this child object |
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Find the SBOL3 TopLevel object containing this SBOL3 object |
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Patch to stabilize order returned in cloning, part of the pySBOL3 issue #231 workaround |
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Change an ontology term into the "standard" form returned by tyto.ontology.get_uri_by_term |
Attributes
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Find the parent of this child object |
- copy_collection_and_dependencies(target, c)
- copy_component_and_dependencies(target, c)
- copy_toplevel_and_dependencies(target, t)
- get_parent(self: sbol3.Identified) Optional[sbol3.Identified]
Find the parent of this child object
- Parameters
self – Object to search from
- Returns
parent or None if it cannot be found (e.g., this is a toplevel)
- get_parent
- get_toplevel(self: sbol3.Identified) Optional[sbol3.TopLevel]
Find the SBOL3 TopLevel object containing this SBOL3 object
- Parameters
self – Object to search from
- Returns
Enclosing TopLevel (self if it is a TopLevel) or None if there is nothing enclosing
- replace_feature(component, old, new)
- sort_owned_objects(self)
Patch to stabilize order returned in cloning, part of the pySBOL3 issue #231 workaround
- string_to_display_id(name: str) str
- type_to_standard_extension
- tyto_lookup_with_caching(term: str) str
- tyto_normalize_term(ontology: tyto.Ontology, uri: str) Optional[str]
Change an ontology term into the “standard” form returned by tyto.ontology.get_uri_by_term Workaround for tyto issue https://github.com/SynBioDex/tyto/issues/75, which will be removed after that issue is addressed.
- Parameters
ontology – Ontology containing term
uri – URI to be normalized
- Returns
normalized URI (or None if term is not in the ontology)