DnaWeaver Reference manual¶
DNA suppliers¶
- class dnaweaver.DnaSupplier[source]¶
Base class for all DnaSuppliers, which are the elements of the supply networks used to define assembly problems in DnaWeaver.
- get_best_lead_time_under_price_limit(sequence, max_price, time_resolution, with_assembly_plan=False)[source]¶
Return the quote with fastest lead time under the budget constraint.
- Parameters:
- sequence (str)
The sequence submitted to the Dna Source for a quote.
- max_price (float)
If provided, the quote returned is the least-lead-time quote whose price is below or equal to max_price. This is done using bisection and can be slow as it requires to re-compute the problem many times. Note that either this parameter or max_lead_time must be None.
- time_resolution
Time resolution for the bisecting search if max_price is not None.
- with_assembly_plan
If True, the assembly plan is added to the quote.
- get_quote(sequence, max_lead_time=None, max_price=None, with_assembly_plan=False, time_resolution=1.0)[source]¶
Return a DnaQuote with price, lead time, etc. for a given sequence.
- Parameters:
- sequence (str)
The sequence submitted to the Dna Source for a quote.
- max_lead_time (float)
If provided, the quote returned is the best quote (price-wise) whose lead time is less or equal to max_lead_time.
- max_price (float)
If provided, the quote returned is the least-lead-time quote whose price is below or equal to max_price. This is done using bisection and can be slow as it requires to re-compute the problem many times. Note that either this parameter or max_lead_time must be None.
- with_assembly_plan
If True, the assembly plan is added to the quote.
- time_resolution
Time resolution for the bisecting search if max_price is not None.
- Returns:
- A DnaQuote object.
- class dnaweaver.DnaSuppliersComparator(suppliers=(), memoize=False, sequence_constraints=(), return_first_accepted_quote=False, name='comparator')[source]¶
Special source that compares quotes from other DnaSuppliers.
Upon receiving a sequence, that source will submit the sequence to Downstream sources, which deliver each one optimal quote. The comparator then returns the one quote with the lowest price.
- Parameters:
- suppliers
List of DnaSuppliers.
- memoize
Whether the quotes should be kept in memory to avoid re-computing the same quote several times. Can accelerate computations but is RAM-expensive.
- get_best_price(sequence, max_lead_time=None, with_assembly_plan=False)[source]¶
Returns a price-optimal DnaQuote for the given sequence.
- Parameters:
- sequence (str)
The sequence submitted to the Dna Source for a quote.
- max_lead_time (float)
If provided, the quote returned is the best quote (price-wise) whose lead time is less or equal to max_lead_time.
- with_assembly_plan
If True, the assembly plan is added to the quote.
- class dnaweaver.DnaAssemblyStation(name, assembly_method, supplier, memoize=False, decomposer_class=None, a_star_auto_multiplier=2, **solver_kwargs)[source]¶
DNA Assembly stations assemble together DNA fragments using a specific assembly method.
- Parameters:
- name
Name of the station (appears on reports).
- assembly_method
A DnaAssemblyMethod object specifying how the fragments are assembled, what sequences can be assembled, what fragments can be used, etc.
- supplier
- memoize
- decomposer_class
- a_star_auto_multiplier
- get_assembly_plan_for_sequence(sequence, max_lead_time=None, coarse_grain=1, fine_grain=1, cut_spread_radius=0, a_star_factor=0, logger=None)[source]¶
Return the plan {(seg, ment): quote, …} of the optimal strategy for the sequence’s decomposition.
- get_assembly_plan_from_cuts(sequence, cuts, max_lead_time=None)[source]¶
Return a plan {segment: quote, …} based on the cut positions.
Where “segment” is of the form (start, end).
- get_best_price(sequence, max_lead_time=None, with_assembly_plan=False)[source]¶
Returns a price-optimal DnaQuote for the given sequence.
- Parameters:
- sequence (str)
The sequence submitted to the Dna Source for a quote.
- max_lead_time (float)
If provided, the quote returned is the best quote (price-wise) whose lead time is less or equal to max_lead_time.
- with_assembly_plan
If True, the assembly plan is added to the quote.