sbol_utilities.expand_combinatorial_derivations
Module Contents
Classes
Class for expanding combinatorial derivations by walking their substructures |
Functions
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Makes a unique display-id for any assignment of values |
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Given a list of CombinatorialDerivations, expand each to make all of the variants that instantiate the |
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Check if the CombinatorialDerivation can be collapsed into a simple Collection of values |
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Main wrapper: read from input file, invoke expand_derivations, then write to output file |
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Find all of the root CombinatorialDerivations in a document (i.e., those not referred to be another CD) |
- class CombinatorialDerivationExpander
Class for expanding combinatorial derivations by walking their substructures
- cd_variable_values(self, v: sbol3.VariableFeature) List[sbol3.Component]
Flatten a variable to collect all of its values
- Parameters
v – Variable to be flattened
- Returns
list of Component values found
- collection_values(self, c: sbol3.Collection) List[sbol3.Component]
Pull all SBOL Components out of a possibly recursive collection
- Parameters
c – Collection for extraction
- Returns
list of Component values found
- derivation_to_collection(self, cd: sbol3.CombinatorialDerivation) sbol3.Collection
Takes a CombinatorialDerivation and list of all those previously expanded, return a Collection of all of the variants generated from the CD, which have been added to its containing document Method: recursively instantiate all variables of the document We’ll do this by a simple depth first search initially, since the numbers shouldn’t be too large
- Parameters
cd – derivation to expand
- Returns
collection of derivative Components
- cd_assigment_to_display_id(cd: sbol3.CombinatorialDerivation, assignment: tuple) str
Makes a unique display-id for any assignment of values
- Parameters
cd – CombinatorialDerivation being expanded
assignment – tuple of variables to expand
- Returns
display ID for this combination
- expand_derivations(targets: List[sbol3.CombinatorialDerivation]) List[sbol3.Collection]
Given a list of CombinatorialDerivations, expand each to make all of the variants that instantiate the specification for each CombinatorialDerivation. All of the expansions are stored in the document. Note: assumes exhaustive sampling strategy
- Parameters
targets – list of CombinatorialDerivations to expand, all of which should be in the same SBOL document
- Returns
list of SBOL Collections, one for each target (in same order as targets)
- is_library(cd: sbol3.CombinatorialDerivation) bool
Check if the CombinatorialDerivation can be collapsed into a simple Collection of values
- Parameters
cd – CombinatorialDerivation being checked
- Returns
true if it can be reduced to a Collection
- main()
Main wrapper: read from input file, invoke expand_derivations, then write to output file
- Returns
None
- root_combinatorial_derivations(doc: sbol3.Document) Set[sbol3.CombinatorialDerivation]
Find all of the root CombinatorialDerivations in a document (i.e., those not referred to be another CD)
- Parameters
doc – Document to search
- Returns
set of root CDs