sbol_utilities.component
Module Contents
Functions
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Pass-through adder for adding a Feature to a Component for allowing slightly more compact code. |
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Compact function for creation of an interaction. |
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Find the features with a given role in the interaction. |
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Creates a Backbone Component and its Sequence. |
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Given an object and a role, check if it is one of the roles of the object. |
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Given an object and a type, check if it is one of the types of the object. |
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Creates a Coding Sequence (CDS) Component and its Sequence. |
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Add a constitutive promoter regulating the target feature. |
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Find the set of all SBOL Components contained within the roots or their children. |
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Assert a topological containment constraint between two features (e.g., a promoter contained in a plasmid). |
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Creates a DNA Component and its Sequence. |
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Creates an ExternallyDefined Protein Component. |
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Creates an ExternallyDefined Restriction Enzyme Component from rebase. |
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Creates an ExternallyDefined Simple Chemical Component. |
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Creates an Engineered Region Component, with features assumed to be in linear order |
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Return a feature associated with the target, i.e., the target itself if a feature, or a SubComponent. |
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Check that the system referred to is unambiguous. Raises ValueError if there are multiple or zero systems. |
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Creates a Component of type functional entity. |
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Creates a Gene Component and its Sequence. |
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Find the (precisely one) feature with a given role in the interaction. |
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Check if an SBOL Component is a DNA Part, i.e., having type 'SBO:DNA', and exactly 1 sequence property |
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Creates a media Component of type functional entity. |
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Creates an mRNA Component and its Sequence. |
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Creates an Operator Component and its Sequence. |
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Assert a topological ordering constraint between two features (e.g., a CDS followed by a terminator). |
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Creates a Part in Backbone Component and its Sequence. |
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Creates a Promoter Component and its Sequence. |
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Creates a Protein Component and its Sequence. |
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Creates a protein stability element Component and its Sequence. |
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Creates a Ribosome Entry Site (RBS) Component and its Sequence. |
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Connect a 5' regulatory region to control the expression of a 3' target region. |
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Creates a RNA Component and its Sequence. |
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Creates a strain Component of type functional entity. |
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Creates a Terminator Component and its Sequence. |
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Creates a Transcription Factor Component and its Sequence. |
- add_feature(component: sbol3.Component, to_add: Union[sbol3.Feature, sbol3.Component]) sbol3.Feature
Pass-through adder for adding a Feature to a Component for allowing slightly more compact code. Note that unlike ensure_singleton_feature, this allows adding multiple instances.
- Parameters
component – Component to add the Feature to
to_add – Feature or Component to be added to system. Components will be wrapped in a SubComponent Feature
- Returns
feature added (SubComponent if to_add was a Component)
- add_interaction(interaction_type: str, participants: Dict[Union[sbol3.Feature, sbol3.Component], str], system: sbol3.Component = None, name: str = None) sbol3.Interaction
Compact function for creation of an interaction. Implicitly identifies system and creates/adds features as necessary.
- Parameters
interaction_type – SBO type of interaction to be to be added
participants – dictionary assigning features/components to roles for participations
system – system to add interaction to
name – name for the interaction
- Returns
interaction
- all_in_role(interaction: sbol3.Interaction, role: str) List[sbol3.Feature]
Find the features with a given role in the interaction.
- Parameters
interaction – interaction to search
role – role to search for
- Returns
sorted list of Features playing that role
- backbone(identity: str, sequence: str, dropout_location: List[int], fusion_site_length: int, linear: bool, **kwargs) Tuple[sbol3.Component, sbol3.Sequence]
Creates a Backbone Component and its Sequence.
- Parameters
identity – The identity of the Component. The identity of Sequence is also identity with the suffix ‘_seq’.
sequence – The DNA sequence of the Component encoded in IUPAC.
dropout_location – List of 2 integers that indicates the start and the end of the dropout sequence including overhangs. Note that the index of the first location is 1, as is typical practice in biology, rather than 0, as is typical practice in computer science.
fusion_site_length – Integer of the lenght of the fusion sites (eg. BsaI fusion site lenght is 4, SapI fusion site lenght is 3)
linear – Boolean than indicates if the backbone is linear, by default it is seted to Flase which means that it has a circular topology.
kwargs – Keyword arguments of any other Component attribute.
- Returns
A tuple of Component and Sequence.
- by_roles(required_role: str) Callable[[sbol3.TopLevel], bool]
Given an object and a role, check if it is one of the roles of the object.
- Parameters
required_role – the role which must be present in given object
- Returns
lambda function taking an obj to check roles in, returns bool
- by_types(required_type: str) Callable[[sbol3.TopLevel], bool]
Given an object and a type, check if it is one of the types of the object.
- Parameters
required_type – the type which must be present in given object
- Returns
lambda function taking an obj to check types in, returns bool
- cds(identity: str, sequence: str, **kwargs) Tuple[sbol3.Component, sbol3.Sequence]
Creates a Coding Sequence (CDS) Component and its Sequence.
- Parameters
identity – The identity of the Component. The identity of Sequence is also identity with the suffix ‘_seq’.
sequence – The DNA sequence of the Component encoded in IUPAC.
kwargs – Keyword arguments of any other Component attribute.
- Returns
A tuple of Component and Sequence.
- constitutive(target: Union[sbol3.Feature, sbol3.Component], system: Optional[sbol3.Component] = None) sbol3.Feature
Add a constitutive promoter regulating the target feature.
- Parameters
target – 5’ region for promoter to regulate
system – optional explicit statement of system
- Returns
newly created constitutive promoter
- contained_components(roots: Union[sbol3.TopLevel, Iterable[sbol3.TopLevel]]) set[sbol3.Component]
Find the set of all SBOL Components contained within the roots or their children. This will explore via all of the direct relations that can include a Component: Collection.member, CombinatorialDerivation.template, variable_features Component.feature:SubComponent, Implementation.built, VariableFeature.variant, variant_derivation, variant_collection
- Parameters
roots – single TopLevel or iterable collection of TopLevel objects to explore
- Returns
set of Components found, including roots
- Raises
TopLevelNotFound – if some referenced Components are not in the document
- contains(container: Union[sbol3.Feature, sbol3.Component], contained: Union[sbol3.Feature, sbol3.Component], system: Optional[sbol3.Component] = None) sbol3.Feature
Assert a topological containment constraint between two features (e.g., a promoter contained in a plasmid). Implicitly identifies system and creates/adds features as necessary.
- Parameters
container – containing feature
contained – feature that is contained
system – optional explicit statement of system
- Returns
contained feature
- dna_component_with_sequence(identity: str, sequence: str, **kwargs) Tuple[sbol3.Component, sbol3.Sequence]
Creates a DNA Component and its Sequence.
- Parameters
identity – The identity of the Component. The identity of Sequence is also identity with the suffix ‘_seq’.
sequence – The DNA sequence of the Component encoded in IUPAC.
kwargs – Keyword arguments of any other Component attribute.
- Returns
A tuple of Component and Sequence.
- ed_protein(definition: str, **kwargs) sbol3.ExternallyDefined
Creates an ExternallyDefined Protein Component.
- Parameters
definition – The URI that links to a canonical definition external to SBOL, recommended UniProt.
kwargs – Keyword arguments of any other ExternallyDefined attribute.
- Returns
A Component object.
- ed_restriction_enzyme(name: str, **kwargs) sbol3.ExternallyDefined
Creates an ExternallyDefined Restriction Enzyme Component from rebase.
- Parameters
name – Name of the SBOL ExternallyDefined, used by PyDNA. Case sensitive, follow standard restriction enzyme nomenclature, i.e. ‘BsaI’
kwargs – Keyword arguments of any other ExternallyDefined attribute.
- Returns
An ExternallyDefined object.
- ed_simple_chemical(definition: str, **kwargs) sbol3.ExternallyDefined
Creates an ExternallyDefined Simple Chemical Component.
- Parameters
definition – The URI that links to a canonical definition external to SBOL, recommended ChEBI and PubChem.
kwargs – Keyword arguments of any other ExternallyDefined attribute.
- Returns
A Component object.
- engineered_region(identity: str, features: Union[List[sbol3.SubComponent], List[sbol3.Component]], **kwargs) sbol3.Component
Creates an Engineered Region Component, with features assumed to be in linear order
- Parameters
identity – The identity of the Component.
features – SubComponents or Components to add as features in linear order
kwargs – Keyword arguments of any other Component attribute.
- Returns
A tuple of Component and Sequence.
- ensure_singleton_feature(system: sbol3.Component, target: Union[sbol3.Feature, sbol3.Component])
Return a feature associated with the target, i.e., the target itself if a feature, or a SubComponent. If the target is not already in the system, add it. Raises ValueError if given a Component with multiple instances.
- Returns
associated feature
- ensure_singleton_system(system: Optional[sbol3.Component], *features: Union[sbol3.Feature, sbol3.Component]) sbol3.Component
Check that the system referred to is unambiguous. Raises ValueError if there are multiple or zero systems.
- Parameters
system – Optional explicit specification of system
features – features in the same system or components to be referenced from it
- Returns
Component for the identified system
- functional_component(identity: str, **kwargs) sbol3.Component
Creates a Component of type functional entity.
- Parameters
identity – The identity of the Component.
kwargs – Keyword arguments of any other Component attribute.
- Returns
A tuple of Component and Sequence.
- gene(identity: str, sequence: str, **kwargs) Tuple[sbol3.Component, sbol3.Sequence]
Creates a Gene Component and its Sequence.
- Parameters
identity – The identity of the Component. The identity of Sequence is also identity with the suffix ‘_seq’.
sequence – The DNA sequence of the Component encoded in IUPAC.
kwargs – Keyword arguments of any other Component attribute.
- Returns
A tuple of Component and Sequence.
- in_role(interaction: sbol3.Interaction, role: str) sbol3.Feature
Find the (precisely one) feature with a given role in the interaction.
- Parameters
interaction – interaction to search
role – role to search for
- Returns
Feature playing that role
- is_dna_part(obj: sbol3.Component) bool
Check if an SBOL Component is a DNA Part, i.e., having type ‘SBO:DNA’, and exactly 1 sequence property
- Parameters
obj – Sbol3 Document to be checked
- Returns
true if dna part
- media(identity: str, recipe: dict[Union[sbol3.Component, sbol3.SubComponent], Union[sbol3.Measure, list]] = None, **kwargs) sbol3.Component
Creates a media Component of type functional entity.
- Parameters
identity – The identity of the Component.
recipe – dictionary of mapping from Component/SubComponent to a quantity (either Measure or value/unit pairs)
kwargs – Keyword arguments of any other Component attribute.
- Returns
a new Component representing the specified media
- Raises
ValueError if there are problems with the recipe elements
- mrna(identity: str, sequence: str, **kwargs) Tuple[sbol3.Component, sbol3.Sequence]
Creates an mRNA Component and its Sequence.
- Parameters
identity – The identity of the Component. The identity of Sequence is also identity with the suffix ‘_seq’.
sequence – The RNA sequence of the Component encoded in IUPAC.
kwargs – Keyword arguments of any other Component attribute.
- Returns
A tuple of Component and Sequence.
- operator(identity: str, sequence: str, **kwargs) Tuple[sbol3.Component, sbol3.Sequence]
Creates an Operator Component and its Sequence.
- Parameters
identity – The identity of the Component. The identity of Sequence is also identity with the suffix ‘_seq’.
sequence – The DNA sequence of the Component encoded in IUPAC.
kwargs – Keyword arguments of any other Component attribute.
- Returns
A tuple of Component and Sequence.
- order(five_prime: Union[sbol3.Feature, sbol3.Component], three_prime: Union[sbol3.Feature, sbol3.Component], system: Optional[sbol3.Component] = None) sbol3.Feature
Assert a topological ordering constraint between two features (e.g., a CDS followed by a terminator). Implicitly identifies system and creates/adds features as necessary.
- Parameters
five_prime – containing feature
three_prime – feature that is contained
system – optional explicit statement of system
- Returns
three_prime feature
- part_in_backbone(identity: str, part: sbol3.Component, backbone: sbol3.Component, linear: bool = False, **kwargs) Tuple[sbol3.Component, sbol3.Sequence]
Creates a Part in Backbone Component and its Sequence.
- Parameters
identity – The identity of the Component. The identity of Sequence is also identity with the suffix ‘_seq’.
part – Part to be located in the backbone as SBOL Component.
backbone – Backbone in wich the part is located as SBOL Component.
linear – Boolean than indicates if the backbone is linear, by default it is seted to Flase which means that it has a circular topology.
kwargs – Keyword arguments of any other Component attribute.
- Returns
A tuple of Component and Sequence.
- promoter(identity: str, sequence: str, **kwargs) Tuple[sbol3.Component, sbol3.Sequence]
Creates a Promoter Component and its Sequence.
- Parameters
identity – The identity of the Component. The identity of Sequence is also identity with the suffix ‘_seq’.
sequence – The DNA sequence of the Component encoded in IUPAC.
kwargs – Keyword arguments of any other Component attribute.
- Returns
A tuple of Component and Sequence.
- protein_component_with_sequence(identity: str, sequence: str, **kwargs) Tuple[sbol3.Component, sbol3.Sequence]
Creates a Protein Component and its Sequence.
- Parameters
identity – The identity of the Component. The identity of Sequence is also identity with the suffix ‘_seq’.
sequence – The Protein sequence of the Component encoded in IUPAC.
kwargs – Keyword arguments of any other Component attribute.
- Returns
A tuple of Component and Sequence.
- protein_stability_element(identity: str, sequence: str, **kwargs) Tuple[sbol3.Component, sbol3.Sequence]
Creates a protein stability element Component and its Sequence.
- Parameters
identity – The identity of the Component. The identity of Sequence is also identity with the suffix ‘_seq’.
sequence – The DNA sequence of the Component encoded in IUPAC.
kwargs – Keyword arguments of any other Component attribute.
- Returns
A tuple of Component and Sequence.
- rbs(identity: str, sequence: str, **kwargs) Tuple[sbol3.Component, sbol3.Sequence]
Creates a Ribosome Entry Site (RBS) Component and its Sequence.
- Parameters
identity – The identity of the Component. The identity of Sequence is also identity with the suffix ‘_seq’.
sequence – The DNA sequence of the Component encoded in IUPAC.
kwargs – Keyword arguments of any other Component attribute.
- Returns
A tuple of Component and Sequence.
- regulate(five_prime: Union[sbol3.Feature, sbol3.Component], target: Union[sbol3.Feature, sbol3.Component], system: Optional[sbol3.Component] = None) sbol3.Feature
Connect a 5’ regulatory region to control the expression of a 3’ target region. Note: this function is an alias for “order”.
- Parameters
five_prime – Regulatory region to place upstream of target
target – region to be regulated (e.g., a CDS or ncRNA)
system – optional explicit statement of system
- Returns
target feature
- rna_component_with_sequence(identity: str, sequence: str, **kwargs) Tuple[sbol3.Component, sbol3.Sequence]
Creates a RNA Component and its Sequence.
- Parameters
identity – The identity of the Component. The identity of Sequence is also identity with the suffix ‘_seq’.
sequence – The RNA sequence of the Component encoded in IUPAC.
kwargs – Keyword arguments of any other Component attribute.
- Returns
A tuple of Component and Sequence.
- strain(identity: str, **kwargs) sbol3.Component
Creates a strain Component of type functional entity.
- Parameters
identity – The identity of the Component.
kwargs – Keyword arguments of any other Component attribute.
- Returns
A Component object.
- terminator(identity: str, sequence: str, **kwargs) Tuple[sbol3.Component, sbol3.Sequence]
Creates a Terminator Component and its Sequence.
- Parameters
identity – The identity of the Component. The identity of Sequence is also identity with the suffix ‘_seq’.
sequence – The DNA sequence of the Component encoded in IUPAC.
kwargs – Keyword arguments of any other Component attribute.
- Returns
A tuple of Component and Sequence.
- transcription_factor(identity: str, sequence: str, **kwargs) Tuple[sbol3.Component, sbol3.Sequence]
Creates a Transcription Factor Component and its Sequence.
- Parameters
identity – The identity of the Component. The identity of Sequence is also identity with the suffix ‘_seq’.
sequence – The Protein amino acid sequence of the Component encoded in IUPAC.
kwargs – Keyword arguments of any other Component attribute.
- Returns
A tuple of Component and Sequence.