Designs

Synbio designs.

Design encode plasmids, libraries (of plasmids) or combinatorial builds for DNA assembly. They are the design specification used for the assembly step.

class synbio.designs.Combinatorial(records: Iterable[Bio.SeqRecord.SeqRecord] = None, linear: bool = True)

A list of SeqRecords. Find and use all valid combinations.

Structure-wise it’s the same as a Plasmid but multiple assemblies are possible given a single set of SeqRecords. List of SeqRecords in, list of SeqRecords out. Versus List of SeqRecords in one SeqRecord out for a Plasmid design

records

list of SeqRecord

linear

Whether the SeqRecords of the design are linear

class synbio.designs.CombinatorialBins(bins: Iterable[List[Bio.SeqRecord.SeqRecord]] = None, linear: bool = True)

A list of bins of SeqRecords. All combinations between bins are attempted.

bins

list of SeqRecord bins

linear

Whether the SeqRecords of the design are linear

append(records: Union[Bio.SeqRecord.SeqRecord, List[Bio.SeqRecord.SeqRecord]])

Add the SeqRecords as a bin for combinatorial design

Parameters

record – the records to add as a bin

class synbio.designs.Plasmid(records: Iterable[Bio.SeqRecord.SeqRecord] = None, linear: bool = True)

Create a plasmid from a list of SeqRecords

records

SeqRecords to concatenate into a plasmid

linear

Whether the SeqRecords of the design are linear

append(records: Union[Bio.SeqRecord.SeqRecord, List[Bio.SeqRecord.SeqRecord]])

Add the SeqRecord to this plasmid’s list of SeqRecords/fragments

Parameters

record – the SeqRecord to add to the plasmid specification

class synbio.designs.PlasmidLibrary(sets: Iterable[List[Bio.SeqRecord.SeqRecord]] = None, linear: bool = True)

A list of SeqRecord lists. Each nested list is combined into a Plasmid.

sets

Iterable of SeqRecord sets

linear

Whether the SeqRecords of the design are linear

append(records: Union[Bio.SeqRecord.SeqRecord, List[Bio.SeqRecord.SeqRecord]])

Add a new set or SeqRecord to the library

Parameters

records – the records to add as a set