API reference¶

main.py¶

Main module for basicsynbio.

This module can import from utils but not from cam or parts_linkers packages.

exception basicsynbio.main.AssemblyException[source]¶

class basicsynbio.main.BasicAssembly(id: str, *parts_linkers: Union[basicsynbio.main.BasicPart, basicsynbio.main.BasicLinker])[source]¶

Class for BASIC DNA assemblies.

Note

BasicAssembly class requires alternating BasicPart and BasicLinker instances in any order.

id¶: Identifier for BasicAssemby object. Must be unique amongst BasicAssembly instances used to initiate a BasicBuild object.

parts_linkers¶: tuple of BasicPart and BasicLinker objects used to create this assembly.

return_clip_reactions() → Tuple[basicsynbio.main.ClipReaction, …][source]¶

A function to return the ClipReaction instances required for BASIC assembly.

Returns: A collection of ClipReaction instances required for BASIC assembly.
Return type: tuple

return_part(**kwargs) → basicsynbio.main.BasicPart [source]¶

A function to return the assembled construct as a new part.

Parameters: kwargs – assigns alternative SeqRecord attributes.
Returns: assembled construct as a new part.
Return type: BasicPart

return_seqrec(**kwargs) → Bio.SeqRecord.SeqRecord[source]¶

A function to return the assembled construct as a seqrecord.

Parameters: kwargs – assigns alternative SeqRecord attributes.
Returns: assembled construct as a new seqrecord.
Return type: seqrec

class basicsynbio.main.BasicLinker(seq: Bio.Seq.Seq, id: str, name: str = None, prefix_id: str = None, suffix_id: str = None, overhang_slice_params: Tuple[int, int] = None, **kwargs)[source]¶

Class for BASIC DNA assembly linkers.

A DNA sequence joined with other BasicLinkers via BasicPart instances when initializing BasicAssembly objects.

prefix_id¶

The prefix half linker id.

Type: str

suffix_id¶

The suffix half linker id.

Type: str

seq¶: Refer to Bio.SeqRecord.SeqRecord documentation.

id¶: Refer to Bio.SeqRecord.SeqRecord documentation.

name¶: This attribute is used to label the annotation in exported gb files or equivalent.

overhang_slice_params¶: Parameters used to slice seq attribute returning overhang sequence. Parameters are in the form (start, stop). Required to access linker_oligos attribute.

linker_oligos¶: Oligonucleotides used to physically generate linker.

basic_slice()[source]¶

The function to obtain the basic slice of BasicLinker objects.

Returns: returns self, the basic slice of BasicLinker objects.
Return type: BasicLinker

property seq¶: The sequence itself, as a Seq or MutableSeq object.

class basicsynbio.main.BasicPart(seq, id: str, **kwargs)[source]¶

Class for BASIC DNA assembly parts.

A DNA sequence joined with other BasicParts via BasicLinker instances when initializing BasicAssembly objects. All sequences must contain intergated prefix and suffix sequences.

_ip_loc¶

The index/location of IP_STR within sequence.

Type: int

_is_loc¶

The index/location of IS_STR within sequence.

Type: int

basic_slice() → Bio.SeqRecord.SeqRecord[source]¶

The Function to obtain region flanked by BASIC iP & iS sequences

Returns: The region flanked by BASIC iP & iS sequences as a SeqRecord object.
Return type: SeqRecord
Raises: ValueError – If iP and iS sequences not correctly identified.

clip_mass(clip_vol: float = 30, circular: bool = True, ndigit: int = None) → Union[float, int][source]¶

Obtain the recommended mass of part (ng) for a clip reaction.

Parameters

clip_vol – volume of the clip reaction (µL).
circular – The part is circular or linear if False.
ndigit – Refer to built-in round function documentation.

domesticating_primers(seq_args: dict = 0, global_args: dict = 0, left_attrs: dict = None, right_attrs: dict = None, primer_pair: int = 0) → basicsynbio.main.DomesticatingPrimers [source]¶

Generate PCR primers and associated data for domesticating parts from various sources using PCR.

PCR primers contain iP and iS sequences, respectively, in addition to a region of homology for the intervening DNA sequence. They can be used to domesticate parts from various sources, adding iP and iS sequences, enabling downstream BASIC assemblies.

Parameters

seq_args – Refer to ‘_primer3py’ method and primer3-py docs.
global_args – Refer to ‘_primer3py’ method and primer3-py docs.
left_attrs – Additional attributes to assign to left_primer SeqRecord.
right_attrs – Additional attributes to assign to the right_primer SeqRecord.
primer_pair – Which of the returned primer3-py primer pairs to use. Defaults to 0 which is the primer pair with the lowest penalty value.

Returns

left_primer & right_primer attributes contain iP & iS sequences, respectively while data corresponds to primer regions homologous to template DNA.

Return type

DomesticatingPrimers

Raises

ValueError – If primer3 fails to identify suitable primer pairs.

property seq¶: The sequence itself, as a Seq or MutableSeq object.

to_seqrec() → Bio.SeqRecord.SeqRecord[source]¶: Create a SeqRecord instance. All relevant attributes are maintained.

class basicsynbio.main.BasicUTRRBSLinker(seq: Bio.Seq.Seq, id: str, name: str, prefix_id: str = None, suffix_id: str = None, **kwargs)[source]¶: Sub-class of BasicLinker for UTR-RBS linkers.

class basicsynbio.main.ClipReaction(prefix, part, suffix)[source]¶

Class for describing clip reactions.

Note

ClipReaction is hashable.

clip_items() → Tuple[basicsynbio.main.BasicLinker, basicsynbio.main.BasicPart, basicsynbio.main.BasicLinker][source]¶

A function to returns a tuple describing each of the items within each clip.

Returns: (prefix linker, part, suffix linker)
Return type: tuple

linker_half_ids() → Tuple[str, str][source]¶

A function to return ids for prefix and suffix linkers in the form (prefix_id, suffix_id).

Returns: returns ids for prefix and suffix linkers in the form (prefix_id, suffix_id).
Return type: tuple

class basicsynbio.main.DomesticatingPrimers(left_primer: Bio.SeqRecord.SeqRecord, right_primer: Bio.SeqRecord.SeqRecord, data: dict)[source]¶

exception basicsynbio.main.LinkerException[source]¶

class basicsynbio.main.LinkerHalfOligos(long: Bio.Seq.Seq, adapter: Bio.Seq.Seq)[source]¶: Oligos used by a linker half.

exception basicsynbio.main.PartException[source]¶

basicsynbio.main.seqrec2part(seqrec: Bio.SeqRecord.SeqRecord, add_i_seqs: bool = False) → basicsynbio.main.BasicPart [source]¶

A function to generate BasicPart instances based on SeqRecords.

Note

Relevant attributes are maintained.

Parameters

seqrec – SeqRecord to be converted to BasicPart subclass.
add_i_seqs – if True adds flanking BASIC iP and iS sequences. Note, letter_annotations attribute is lost.

Returns

BasicPart instance of seqrec.

Return type

BasicPart

bsb_io.py¶

Module contains objects for importing and exporting parts and sequences.

basicsynbio.bsb_io.export_sequences_to_file(sequences: Iterable[Union[Bio.SeqRecord.SeqRecord, basicsynbio.main.BasicPart, basicsynbio.main.BasicAssembly]], handle: str, format: str = 'genbank', molecule_type: str = 'DNA') → None[source]¶

Exports sequences to file using Bio.SeqIO.write().

Note

Refer to Biopython documentation for further information on Bio.SeqIO.write().

Parameters

sequences – Sequences to export.
handle – handle to file.
format – file format.
molecule_type (optional) – Type of molecule within sequences. defaults to ‘DNA’.

Raises

ValueError – sequences was not of correct type.

basicsynbio.bsb_io.import_part(handle: str, format: str, add_i_seqs: bool = False) → basicsynbio.main.BasicPart [source]¶

Imports a Part object using Bio.SeqIO.read().

Note

Refer to Biopython documentation for further information on Bio.SeqIO.read().

Parameters

handle – handle to file.
format – file format.
add_i_seqs – if True adds flanking BASIC iP and iS sequences. Note, letter_annotations attribute is lost.

Returns

a BASIC DNA assembly part.

Return type

BasicPart

basicsynbio.bsb_io.import_parts(handle: str, format: str, add_i_seqs=False) → Iterable[basicsynbio.main.BasicPart][source]¶

Imports a Generator of BasicPart objects using Bio.SeqIO.parse().

Note

Refer to Biopython documentation for further information on Bio.SeqIO.parse().

Parameters

handle – handle to file.
format – file format.
add_i_seqs – if True adds flanking BASIC iP and iS sequences. Note, letter_annotations attribute is lost.

Yields

BasicPart – all parts within the file handle.

basicsynbio.bsb_io.import_sbol_parts(path: str, add_i_seqs=False) → Generator[basicsynbio.main.BasicPart, None, None][source]¶

Imports BasicPart objects using sbol2.Document.exportToFormat.

Note

Refer to Biopython documentation for further information on Bio.SeqIO.read(). Refer to pysbol2 documentation for further information.

Parameters

path – path to SBOL file.
add_i_seqs – if True adds flanking BASIC iP and iS sequences. Note, letter_annotations attribute is lost.

Yields

BasicPart – all parts within the file handle.

cam.main.py¶

Module contains key objects for computer assisted manufacturing (CAM) within the BASIC DNA assembly framework.

class basicsynbio.cam.main.BasicBuild(*basic_assemblies: basicsynbio.main.BasicAssembly)[source]¶

Class provides methods and attributes for building BasicAssembly objects.

basic_assemblies¶: Tuple of BasicAssembly objects used to initiate BasicBuild.

unique_clips¶: Tuple of unique ClipReaction objects required to implement the build.

clips_data¶: A dictionary with each ClipReaction as a key and BasicAssembly objects that require it as values.

unique_parts¶: Tuple of the unique BasicPart object required to implement the build.

unique_linkers¶: Tuple of the unique BasicLinker objects required to implement the build.

update_parts(*parts: basicsynbio.main.BasicPart) → None[source]¶

Updates BasicBuild instance with parts.

Replaces all existing BasicParts used in assemblies with the matching equivalent in parts.

Parameters: parts – parts to replace the BasicParts used in assemblies
Raises: ValueError – if length parts is not equal to length this build’s unique parts

class basicsynbio.cam.main.BuildDecoder[source]¶

A Class to decode json dictionary to basicsynbio objects, extending json.JSONDecoder class

decode_build(dictionary: dict) → basicsynbio.cam.main.BasicBuild [source]¶

A method to return BasicBuild from encoded json object

Parameters: dictionary – json object encoded by BuildEncoder
Returns: BasicBuild object built from encoded json
Return type: BasicBuild

return_basic_assemblies(dictionary: dict) → Generator[basicsynbio.main.BasicAssembly, None, None][source]¶

A method to yield BasicAssembly objects from encoded json object

Parameters: dictionary – json object encoded by BuildEncoder
Yields: BasicAssembly – BasicAssembly objects within encoded BasicBuild

static return_unique_linkers(dictionary)[source]¶

A method to return unqiue BasicLinker objects from encoded json object

Parameters: dictionary – json object encoded by BuildEncoder
Returns: containing unique BasicLinker objects
Return type: dictionary

static return_unqiue_parts(dictionary)[source]¶

A method to return unique BasicPart objects from encoded json object

Parameters: dictionary – json object encoded by BuildEncoder
Returns: containing unique BasicPart objects
Return type: dictionary

class basicsynbio.cam.main.BuildEncoder(*, skipkeys=False, ensure_ascii=True, check_circular=True, allow_nan=True, sort_keys=False, indent=None, separators=None, default=None)[source]¶

A Class to encode BasicBuild objects extending json.JSONEncoder class

static assembly_data_json(obj)[source]¶

A function to create machine readable json objects, completely describing BasicAssembly objects within BasicBuild.

Parameters: obj – BasicBuild object to be decoded
Returns: returns a list of dictionaries populated by dictionaries with items describing BasicAssemblies generated by the build.
Return type: list

static clips_data_json(obj)[source]¶

A function to create machine readable json objects, completely describing ClipReaction objects within BasicBuild.

Parameters: obj – BasicBuild object to be decoded
Returns: Each item describes a given unique ClipReaction object required for the build.
Return type: dictionary

default(obj)[source]¶

Implement this method in a subclass such that it returns a serializable object for o, or calls the base implementation (to raise a TypeError).

For example, to support arbitrary iterators, you could implement default like this:

def default(self, o):
    try:
        iterable = iter(o)
    except TypeError:
        pass
    else:
        return list(iterable)
    # Let the base class default method raise the TypeError
    return JSONEncoder.default(self, o)

static unique_linkers_json(obj)[source]¶

A function to create machine readable json objects, completely describing unique linkers.

Parameters: obj – BasicBuild object to be decoded
Returns: Each item describes a given unique BasicLinker object required for the build.
Return type: dictionary

static unique_parts_json(obj)[source]¶

A function to create machine readable json objects, completely describing unique parts.

Parameters: obj – BasicBuild object to be decoded
Returns: Each item describes a unique BasicPart object required for the build.
Return type: dictionary

exception basicsynbio.cam.main.BuildException[source]¶

decorators.py¶

Module contains decorators.

class basicsynbio.decorators.ArgDescription(argument: str, description: str)[source]¶: Class for documenting arguments.

basicsynbio.decorators.addargs2docs(*arg_descriptions: basicsynbio.decorators.ArgDescription)[source]¶

Decorator for adding argument docstrings to functions.

Note

Arguments for documentation must be given in the function docstring with a blank description.

Parameters: arg_descriptions – The argument to document and its description.
Returns: Decorator.

pdf_instructions.py¶

basicsynbio.cam.pdf_instructions.pdf_instructions(basic_build: basicsynbio.cam.main.BasicBuild, path: str = None, assemblies_per_clip: int = 28)[source]¶

Writes instructions to implement build to a pdf file.

Parameters

basic_build – BasicBuild object the pdf lab instructions are written for.
path (optional) – path to pdf file. If none defaults to working directory with a time stamped name.
assemblies_per_clip (optional) – number of assemblies each purified clip reaction can support.

Returns

filepath of created pdf

Return type

str

echo_instructions.py¶

basicsynbio.cam.echo_instructions.export_echo_assembly(basic_build: basicsynbio.cam.main.BasicBuild, path: str = None, buffer_well: str = 'A1', water_well: str = 'B1', alternate_well: bool = False, assemblies_per_clip: int = 20, clips_plate_size: Literal[6, 24, 96, 384, 1536] = 384, assemblies_plate_size: Literal[6, 24, 96, 384, 1536] = 96) → None[source]¶

Writes automation scripts for a echo liquid handler to build assemblies from clips.

Parameters

path (optional) – path to zipped folder of csv files. If none defaults to working directory with a time stamped name, output csvs is created.
buffer_well (optional) – location in 6 well plate of assembly buffer.
water_well (optional) – location in 6 well plate of dH20.
alternate_well (optional) – specifies whether alternating wells are to be used in the input 384 well plate.
assemblies_per_clip (optional) – number of assemblies each purified clip reaction can support.
clips_plate_size (optional) – specifies the size of the clips plate. Defaults to 384
assemblies_plate_size (optional) – specifiesthe size of the assemblies plates. Defaults to 96

Returns

Path of zip file containing echo automation scripts

Return type

str

Raises

ValueError – If water_well or buffer_well is not in [“A1”, “B1”, “A2”, “B2”, “A3”, “B3”]; if self contains 96 or more assemblies or if the build requires equal or more than 384 used clip wells for alternate_well(True) or 192 for alternate_well(False).

API reference¶

main.py¶

bsb_io.py¶

cam.main.py¶

decorators.py¶

pdf_instructions.py¶

echo_instructions.py¶

basicsynbio

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