Useful methods built on top of DNA Cauldron¶
-
dnacauldron.utils.
list_overhangs_from_record_annotations
(rec, with_locations=False)[source]¶ Return a least of the (probable) overhangs used building the construct
-
dnacauldron.utils.
list_digestion_overhangs
(records, enzyme='auto', parts_only=True)[source]¶ List all overhangs created by restriction in the provided records.
Warning: only overhangs on non-reversed fragments are returned, not their reverse-complement.
- Parameters
- records
List of records
- enzyme
Either ‘BsmBI’, ‘BsaI’, etc. or just “auto” for automatic selection.
- parts_only
If true, overhangs created by restriction which are not on a part (so for instance inside a backbone) will be ignored.
-
dnacauldron.utils.
substitute_overhangs
(record, substitutions, enzyme='auto', return_linear_parts=False)[source]¶ Replace the record’s subsequence that corresponds to overhangs.
This is practical to change the position of a part in a Type-2S assembly standard
- Parameters
- record
A Biopython record whose internal sequence needs to be replaced
- substitutions
A dict {overhang: new_overhang} of which overhangs must be replaced
- enzyme
Either ‘BsmBI’, ‘BsaI’, etc. or just “auto” for automatic selection.
Examples
>>> new_record = replace_overhangs(record, {'ATGC': 'CTCG'})
-
dnacauldron.utils.
swap_donor_vector_part
(donor_vector, insert, enzyme, allow_overhangs_edits=False)[source]¶ Return the records obtained by cloning inserts into a donor vector.
Meant for Type-2S assembly standards only (Golden Gate, etc.)
This method is meant to quickly go from a linearized sequence of a part to a circular vector (the part in its donor vector) by starting from an existing donor vector (with same overhangs) and swapping this vector’s part for the insert of interest.
- Parameters
- donor_vector
Biopython record of a donor vector. must have an insert producing a restriction-free fragment
- insert
Biopython record of a plasmid or a linear DNA sequence containing an insert (i.e. a fragment that is cut out)
- enzyme
The name of the enzyme to use e.g. ‘BsmBI’, ‘BsaI’, …
-
dnacauldron.utils.
insert_parts_on_backbones
(part_records, backbone_records, enzyme='autodetect', min_backbone_length=500, process_parts_with_backbone=False, default_backbone_choice=None)[source]¶ Autodetect the right backbone for each Golden Gate part.
This method is meant to process a batch of genbank files, some of which might represent a part on a backbone, and some of which represent simply a part (and enzyme-flanked overhangs) which needs to be complemented with the right backbone.
It will return, for each part, whether it has already a backbone, and if not, which backbone was selected and what the final sequence is.
- Parameters
- part_records
List of genbanks of the parts to put on vectors.
- backbone_vectors
Vectors to insert parts in, typically donor vectors for different positions of an assembly standard.
- enzyme
Enzyme to use. Use autodetect for autodetection.
- min_backbone_length
Minimal length of a backbone. Used to determine if a part is represented alone or with a backbone.
- process_parts_with_backbone
If true, parts will be inserted in an autoselected backbone even when they already have a backbone (it will be replaced).
-
dnacauldron.utils.
record_contains_backbone
(record, enzyme='BsmBI', min_backbone_length=500)[source]¶ Return True iff it believes the given record contains a backbone.
A backbone is detected if, when cutting the circularized record with the given enzyme, there is one fragment with no site (the insert), and the rest has a total size above the given
min_backbone_length
.
-
class
dnacauldron.utils.
BackboneChoice
(record, already_on_backbone=None, error=None, backbone_record=None, final_record=None)[source]¶ Class to represent the result of a backbone autoselection.
- Parameters
- record
Record that was analyzed, containing an insert, to be backbonized, and potentially an original backbone too.
- already_on_backbone
Was a backbone detected in that record ?
- error
- backbone_record
Record of the backone that was selected for this record among all provided choices.
- final_record
Record featuring the original insert in the given
record
cloned into the auto-selected backbone.