Haploid Organisms¶
- class co.organism.FeatureView(components)¶
Iterates over all features in a set of components – not necessarily in order – and provides search access to these features.
- find(**kwargs)¶
Searches all components and yields features matching the constraints.
See also
feature.FeatureSet.find()
- class co.organism.HaploidOrganism(id, parent=None)¶
- id¶
ID of the organism
- parent¶
Parent organism
- diff(other)¶
Parameters: other (HaploidOrganism) – Returns: A Diff object with added, changed, and removed component names.
- fdiff(other)¶
Returns: A Diff object with added and removed features.
- features¶
A read-only view of all the features present in all components of the organism.
Returns: FeatureView
- get_lineage(inclusive=True)¶
Iterate over all ancestors of this organism
Parameters: inclusive (bool) – whether to include the organism itself in the lineage Returns: iterator over HaploidOrganism objects
- remove(name)¶
Parameters: name (str) – key of the component to remove
- set(name, component)¶
Parameters: - name (str) – key for this component e.g. 'genome', 'chr1', or 'pLASMID'
- component (Component) –