An implementation of the CIDAR ToolKit for the Python MoClo library.
References
moclo.kits.cidar.
CIDARProduct
(Product)[source]¶A CIDAR MoClo product.
__init__
(record)¶Initialize self. See help(type(self)) for accurate signature.
cutter
¶alias of Bio.Restriction.Restriction.BbsI
is_valid
()¶Check if the wrapped record follows the required class structure.
Returns: | True if the record is valid, False otherwise. |
---|---|
Return type: | bool |
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 |
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:
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.
moclo.kits.cidar.
CIDAREntryVector
(EntryVector)[source]¶A CIDAR MoClo entry vector.
__init__
(record)¶Initialize self. See help(type(self)) for accurate signature.
assemble
(module, *modules, **kwargs)¶Assemble the provided modules into the vector.
Parameters: |
|
---|---|
Returns: | the assembled sequence with sequence annotations inherited from the vector and the modules. |
Return type: |
|
Raises: |
|
cutter
¶alias of Bio.Restriction.Restriction.BbsI
is_valid
()¶Check if the wrapped record follows the required class structure.
Returns: | True if the record is valid, False otherwise. |
---|---|
Return type: | bool |
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.
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:
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).
moclo.kits.cidar.
CIDAREntry
(Entry)[source]¶A CIDAR MoClo entry.
__init__
(record)¶Initialize self. See help(type(self)) for accurate signature.
cutter
¶alias of Bio.Restriction.Restriction.BsaI
is_valid
()¶Check if the wrapped record follows the required class structure.
Returns: | True if the record is valid, False otherwise. |
---|---|
Return type: | bool |
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 |
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:
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.
moclo.kits.cidar.
CIDARCassetteVector
(CassetteVector)[source]¶A CIDAR Moclo cassette vector.
References
Iverson et al., Figure 1.
__init__
(record)¶Initialize self. See help(type(self)) for accurate signature.
assemble
(module, *modules, **kwargs)¶Assemble the provided modules into the vector.
Parameters: |
|
---|---|
Returns: | the assembled sequence with sequence annotations inherited from the vector and the modules. |
Return type: |
|
Raises: |
|
cutter
¶alias of Bio.Restriction.Restriction.BsaI
is_valid
()¶Check if the wrapped record follows the required class structure.
Returns: | True if the record is valid, False otherwise. |
---|---|
Return type: | bool |
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.
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:
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).
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.
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.
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.
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.
moclo.kits.cidar.
CIDARDeviceVector
(DeviceVector)[source]¶A CIDAR Moclo device vector.
References
Iverson et al., Figure 1.
cutter
¶alias of Bio.Restriction.Restriction.BbsI
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: