CIDAR Kit¶
An implementation of the CIDAR ToolKit for the Python MoClo library.
References
Level -1¶
Module¶
- class moclo.kits.cidar.CIDARProduct(Product)[source]¶
A CIDAR MoClo product.
- __init__(record)¶
- cutter¶
alias of
Bio.Restriction.Restriction.BbsI
- is_valid()¶
Check if the wrapped record follows the required class structure.
- overhang_end()¶
Get the downstream overhang of the target sequence.
- Returns
the downstream overhang.
- Return type
Seq
- overhang_start()¶
Get the upstream overhang of the target sequence.
- Returns
the downstream overhang.
- Return type
Seq
- classmethod structure()¶
Get the module structure, as a DNA regex pattern.
Warning
If overloading this method, the returned pattern must include 3 capture groups to capture the following features:
The upstream (5’) overhang sequence
The module target sequence
The downstream (3’) overhang sequence
- target_sequence()¶
Get the target sequence of the module.
Modules are often stored in a standardized way, and contain more than the sequence of interest: for instance they can contain an antibiotic marker, that will not be part of the assembly when that module is assembled into a vector; only the target sequence is inserted.
- Returns
the target sequence with annotations.
- Return type
SeqRecord
Note
Depending on the cutting direction of the restriction enzyme used during assembly, the overhang will be left at the beginning or at the end, so the obtained record is exactly the sequence the enzyme created during restriction.
Vector¶
- class moclo.kits.cidar.CIDAREntryVector(EntryVector)[source]¶
A CIDAR MoClo entry vector.
- __init__(record)¶
- assemble(module, *modules, **kwargs)¶
Assemble the provided modules into the vector.
- Parameters
module (
AbstractModule
) – a module to insert in the vector.modules (
AbstractModule
, optional) – additional modules to insert in the vector. The order of the parameters is not important, since modules will be sorted by their start overhang in the function.
- Returns
the assembled sequence with sequence annotations inherited from the vector and the modules.
- Return type
SeqRecord
- Raises
DuplicateModules – when two different modules share the same start overhang, leading in possibly non-deterministic constructs.
MissingModule – when a module has an end overhang that is not shared by any other module, leading to a partial construct only
InvalidSequence – when one of the modules does not match the required module structure (missing site, wrong overhang, etc.).
UnusedModules – when some modules were not used during the assembly (mostly caused by duplicate parts).
- cutter¶
alias of
Bio.Restriction.Restriction.BbsI
- is_valid()¶
Check if the wrapped record follows the required class structure.
- overhang_end()¶
Get the downstream overhang of the vector sequence.
- overhang_start()¶
Get the upstream overhang of the vector sequence.
- placeholder_sequence()¶
Get the placeholder sequence in the vector.
The placeholder sequence is replaced by the concatenation of modules during the assembly. It often contains a dropout sequence, such as a GFP expression cassette that can be used to measure the progress of the assembly.
- static structure()[source]¶
Get the vector structure, as a DNA regex pattern.
Warning
If overloading this method, the returned pattern must include 3 capture groups to capture the following features:
The downstream (3’) overhang sequence
The vector placeholder sequence
The upstream (5’) overhang sequence
- target_sequence()¶
Get the target sequence in the vector.
The target sequence if the part of the plasmid that is not discarded during the assembly (everything except the placeholder sequence).
Level 0¶
Module¶
- class moclo.kits.cidar.CIDAREntry(Entry)[source]¶
A CIDAR MoClo entry.
- __init__(record)¶
- cutter¶
alias of
Bio.Restriction.Restriction.BsaI
- is_valid()¶
Check if the wrapped record follows the required class structure.
- overhang_end()¶
Get the downstream overhang of the target sequence.
- Returns
the downstream overhang.
- Return type
Seq
- overhang_start()¶
Get the upstream overhang of the target sequence.
- Returns
the downstream overhang.
- Return type
Seq
- classmethod structure()¶
Get the module structure, as a DNA regex pattern.
Warning
If overloading this method, the returned pattern must include 3 capture groups to capture the following features:
The upstream (5’) overhang sequence
The module target sequence
The downstream (3’) overhang sequence
- target_sequence()¶
Get the target sequence of the module.
Modules are often stored in a standardized way, and contain more than the sequence of interest: for instance they can contain an antibiotic marker, that will not be part of the assembly when that module is assembled into a vector; only the target sequence is inserted.
- Returns
the target sequence with annotations.
- Return type
SeqRecord
Note
Depending on the cutting direction of the restriction enzyme used during assembly, the overhang will be left at the beginning or at the end, so the obtained record is exactly the sequence the enzyme created during restriction.
Vector¶
- class moclo.kits.cidar.CIDARCassetteVector(CassetteVector)[source]¶
A CIDAR Moclo cassette vector.
References
Iverson et al., Figure 1.
- __init__(record)¶
- assemble(module, *modules, **kwargs)¶
Assemble the provided modules into the vector.
- Parameters
module (
AbstractModule
) – a module to insert in the vector.modules (
AbstractModule
, optional) – additional modules to insert in the vector. The order of the parameters is not important, since modules will be sorted by their start overhang in the function.
- Returns
the assembled sequence with sequence annotations inherited from the vector and the modules.
- Return type
SeqRecord
- Raises
DuplicateModules – when two different modules share the same start overhang, leading in possibly non-deterministic constructs.
MissingModule – when a module has an end overhang that is not shared by any other module, leading to a partial construct only
InvalidSequence – when one of the modules does not match the required module structure (missing site, wrong overhang, etc.).
UnusedModules – when some modules were not used during the assembly (mostly caused by duplicate parts).
- cutter¶
alias of
Bio.Restriction.Restriction.BsaI
- is_valid()¶
Check if the wrapped record follows the required class structure.
- overhang_end()¶
Get the downstream overhang of the vector sequence.
- overhang_start()¶
Get the upstream overhang of the vector sequence.
- placeholder_sequence()¶
Get the placeholder sequence in the vector.
The placeholder sequence is replaced by the concatenation of modules during the assembly. It often contains a dropout sequence, such as a GFP expression cassette that can be used to measure the progress of the assembly.
- static structure()[source]¶
Get the vector structure, as a DNA regex pattern.
Warning
If overloading this method, the returned pattern must include 3 capture groups to capture the following features:
The downstream (3’) overhang sequence
The vector placeholder sequence
The upstream (5’) overhang sequence
- target_sequence()¶
Get the target sequence in the vector.
The target sequence if the part of the plasmid that is not discarded during the assembly (everything except the placeholder sequence).
Parts¶
- class moclo.kits.cidar.CIDARPromoter(CIDARPart, CIDAREntry)[source]¶
A CIDAR Promoter part.
Parts of this type contain contain a promoter. The upstream overhangs can be changed to amend the order of assembly of a circuit from different cassettes.
Note
The CIDAR toolkit parts provide 4 different upstream overhangs: GGAG, GCTT, CGCT, and TGCC. These are not enforced in this module, and any upstream sequence will be accepted. The downstream sequence however is always TACT.
- class moclo.kits.cidar.CIDARRibosomeBindingSite(CIDARPart, CIDAREntry)[source]¶
A CIDAR ribosome binding site.
Parts of this type contain a ribosome binding site (RBS). The downstream overhang doubles as the start codon for the subsequent coding sequence.
- class moclo.kits.cidar.CIDARCodingSequence(CIDARPart, CIDAREntry)[source]¶
A CIDAR coding sequence.
Parts of this type contain a coding sequence, with the start codon located on the upstream overhang.
Caution
Although the start codon is located on the upstream overhang, a STOP codon is expected to be found within this part target sequence before the downstream overhang.
- class moclo.kits.cidar.CIDARTerminator(CIDARPart, CIDAREntry)[source]¶
A CIDAR terminator.
Parts of this type contain a terminator. The upstream overhang is always the same for the terminator to directly follow the coding sequence, but the downstream overhang can vary to specify an order for a following multigenic assembly within a device.
Note
The CIDAR toolkit parts provide 4 different downstream overhangs: GCTT, CGCT, TGCC, and ACTA. These are not enforced in this module, and any downstream sequence will be accepted. The upstream sequence however is always AGGT.
Level 1¶
Module¶
Vector¶
- class moclo.kits.cidar.CIDARDeviceVector(DeviceVector)[source]¶
A CIDAR Moclo device vector.
References
Iverson et al., Figure 1.
- cutter¶
alias of
Bio.Restriction.Restriction.BbsI
- static structure()[source]¶
Get the vector structure, as a DNA regex pattern.
Warning
If overloading this method, the returned pattern must include 3 capture groups to capture the following features:
The downstream (3’) overhang sequence
The vector placeholder sequence
The upstream (5’) overhang sequence