An implementation of the EcoFlex ToolKit for the Python MoClo library.
References
moclo.kits.ecoflex.
EcoFlexEntry
(Entry)[source]¶An EcoFlex MoClo entry.
EcoFlex entries are stored and shared as plasmids flanked by BsaI binding sites at both ends of the target sequence.
__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.ecoflex.
EcoFlexCassetteVector
(CassetteVector)[source]¶An EcoFlex MoClo cassette 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.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.ecoflex.
EcoFlexPromoter
(EcoFlexPart, EcoFlexEntry)[source]¶An EcoFlex MoClo promoter.
moclo.kits.ecoflex.
EcoFlexRBS
(EcoFlexPart, EcoFlexEntry)[source]¶An EcoFlex MoClo ribosome binding site.
Parts of this type contain a ribosome binding site (RBS). The last adenosine serves as the beginning of the start codon of the following CDS.
moclo.kits.ecoflex.
EcoFlexTagLinker
(EcoFlexPart, EcoFlexEntry)[source]¶An EcoFlex MoClo tag linker.
Parts of this type also contain a RBS, but they allow adding a N-terminal tag sequence before the CDS.
moclo.kits.ecoflex.
EcoFlexTag
(EcoFlexPart, EcoFlexEntry)[source]¶An EcoFlex MoClo N-terminal tag.
Parts of this type typically contain tags that are added to the N-terminus of the translated protein, such as a hexa histidine or a Strep(II) tag.
moclo.kits.ecoflex.
EcoFlexCodingSequence
(EcoFlexPart, EcoFlexEntry)[source]¶An EcoFlex MoClo coding sequence.
Parts of this type contain a coding sequence (CDS), with the start codon beginning 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.ecoflex.
EcoFlexDeviceVector
(DeviceVector)[source]¶An EcoFlex MoClo device vector.
cutter
¶alias of Bio.Restriction.Restriction.BsmBI
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: