dasi.design.LibraryDesign¶

class dasi.design.LibraryDesign(span_cost=None, seqdb=None)[source]¶

Bases: dasi.design.designabc.DesignABC

Design class for producing assemblies for libraries.

Something.

Methods

`_expand_from_synthesized`()	Expand PCR products that are next to SYNTHESIZED_FRAGMENTS.
`_expand_synthesized_fragments`()	copy groups from SHARED_FRAGMENTS to SYNTHESIZED_FRAGMENT
`_optimize`(n_paths)	Finds the optimal paths for each query in the design.
`_run`(n_paths, post_processing_kwargs)	Run the design.
`_share_query_blast`()	Find and use shared fragments across queries.
`add_fragments`(fragments)	Add fragment sequences to materials list.
`add_primers`(primers)	Add primer sequences to materials list.
`add_queries`(queries)	Add goal/query sequences to materials list.
`add_templates`(templates)	Add template sequences to materials list.
`assemble_graphs`([query_keys])	Assemble all assembly graphs for all queries in this design.
`compile`([post_process_kwargs])	Compile the materials list into assembly graphs.
`filter_linear_records`(records)	Return only linear records.
`filter_perfect_subject`(results)	return only results whose subject is 100% aligned to query.
`out`([fmt, elim_extra_reactions, query_keys])	Return the results of the design as a validates output JSON.
`out_jsonschema`()	Return the output JSONschema.

Attributes

`container_list`	List of alignment containers in this design.
`containers`	Iterable of alignment containers in this design.
`is_compiled`	Return whether the design has been compiled.
`query_keys`	List of query keys in this design.
`status`	Return the statuses for each subdesign.

__init__(span_cost=None, seqdb=None)[source]¶: Something.

Methods

`__init__`([span_cost, seqdb])	Something.
`add_fragments`(fragments)	Add fragment sequences to materials list.
`add_materials`(primers, templates, queries[, …])
`add_primers`(primers)	Add primer sequences to materials list.
`add_queries`(queries)	Add goal/query sequences to materials list.
`add_templates`(templates)	Add template sequences to materials list.
`assemble_graphs`([query_keys])	Assemble all assembly graphs for all queries in this design.
`compile`([post_process_kwargs])	Compile the materials list into assembly graphs.
`fake`(circular, n_cyclic_seqs, n_linear_seqs, …)
`filter_linear_records`(records)	Return only linear records.
`filter_perfect_subject`(results)	return only results whose subject is 100% aligned to query.
`optimize`([n_paths])	rtype `Dict`[`str`, `DesignResult`]
`out`([fmt, elim_extra_reactions, query_keys])	Return the results of the design as a validates output JSON.
`path_to_edge_costs`(path, graph)	rtype `List`[`Tuple`[`AssemblyNode`, `AssemblyNode`, `dict`]]
`post_process_graphs`([post_processor_kwargs])
`report`()
`run`([n_paths, post_processing_kwargs, …])
`to_df`([assembly_index])	rtype `Tuple`[`DataFrame`, `DataFrame`]
`update_library_metadata`()

Attributes

`ALGORITHM`
`DEFAULT_N_ASSEMBLIES`
`DEFAULT_N_JOBS`
`FAVOR_SHARED_SEQUENCES`
`FRAGMENTS`
`PRIMERS`
`QUERIES`
`TEMPLATES`
`container_list`	List of alignment containers in this design.
`containers`	Iterable of alignment containers in this design.
`is_compiled`	Return whether the design has been compiled.
`last_compile_end`
`last_compile_start`
`last_run_end`
`last_run_start`
`metadata`
`query_keys`	List of query keys in this design.
`results`
`seqdb`	rtype `Dict`[`str`, `SeqRecord`]
`status`	Return the statuses for each subdesign.

_expand_from_synthesized()[source]¶

Expand PCR products that are next to SYNTHESIZED_FRAGMENTS.

Returns

_expand_synthesized_fragments()[source]¶

copy groups from SHARED_FRAGMENTS to SYNTHESIZED_FRAGMENT
expand overlaps for SYNTHESIZED_FRAGMENTS

_optimize(n_paths)¶

Finds the optimal paths for each query in the design.

Return type: Dict[str, DesignResult]

_run(n_paths, post_processing_kwargs)¶

Run the design. Runs compile and optimize, returning results that can be accessed by design.results or by design.out()

Parameters: n_paths (int) – max number of assemblies per design to design
Returns: results

_share_query_blast()[source]¶

Find and use shared fragments across queries.

Returns

add_fragments(fragments)¶: Add fragment sequences to materials list.

add_primers(primers)¶: Add primer sequences to materials list.

add_queries(queries)¶: Add goal/query sequences to materials list.

add_templates(templates)¶: Add template sequences to materials list.

assemble_graphs(query_keys=None)¶: Assemble all assembly graphs for all queries in this design.

compile(post_process_kwargs=None)¶: Compile the materials list into assembly graphs.

property container_list¶

List of alignment containers in this design.

Return type: List[AlignmentContainer]

property containers¶

Iterable of alignment containers in this design.

Return type: Dict[str, AlignmentContainer]

classmethod filter_linear_records(records)¶

Return only linear records.

Return type: List[SeqRecord]

classmethod filter_perfect_subject(results)¶

return only results whose subject is 100% aligned to query.

Return type: List[dict]

property is_compiled¶

Return whether the design has been compiled.

Returns: True if compiled. False if otherwise.

out(fmt='json', elim_extra_reactions=False, query_keys=None)¶

Return the results of the design as a validates output JSON.

The output JSON is follows the following schema, see :type fmt: str :param fmt: :return:

out_jsonschema()¶: Return the output JSONschema.

property query_keys¶

List of query keys in this design.

Return type: List[str]

property status¶: Return the statuses for each subdesign.