sbol_utilities.calculate_sequences
Module Contents
Functions
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Attempt to calculate missing sequences of Components from their features |
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Compute the sequence of a component and add this information into the Component in place |
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Main wrapper: read from input file, invoke calculate_sequences, then write to output file |
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Attempt to find a sorted order of features in an SBOL Component, so its sequence can be calculated from theirs |
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Check if a DNA component still needs its sequence calculated |
- calculate_sequences(doc: sbol3.Document) List[sbol3.Sequence]
Attempt to calculate missing sequences of Components from their features
- Parameters
doc – Document where sequences will be calculated
- Returns
list of newly computed sequences
- compute_sequence(component: sbol3.Component) sbol3.Sequence
Compute the sequence of a component and add this information into the Component in place
- Parameters
component – Component whose sequence is to be computed
- Returns
Sequence that has been computed
- main()
Main wrapper: read from input file, invoke calculate_sequences, then write to output file
- order_subcomponents(component: sbol3.Component) Union[Tuple[List[sbol3.Feature], bool], None]
Attempt to find a sorted order of features in an SBOL Component, so its sequence can be calculated from theirs Conduct the sort by walking through one meet relation at a time (excepting a circular component)
- Parameters
component – Component whose features are to be oreered
- Returns
if the features can be ordered, return a list of features in the order that they should be joined and
a boolean indicating if it’s circular. If the features cannot be ordered, return None
- ready_to_resolve(component: sbol3.Component, resolved: Iterable[str])
- resolved_dna_component(component: sbol3.Component) bool
Check if a DNA component still needs its sequence calculated
- Parameters
component – SBOL Component to check
- Returns
True if it has a DNa sequence; false otherwise