assemble_operon
Stack several CDSs into one contiguous operon, designing a fresh ribosome-binding site in front of each one AGAINST ITS REAL UPSTREAM CONTEXT — which is why the RBS for gene 2 is not the RBS design_rbs would give it in isolation.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| cds | Yes | the coding sequences to stack, in order — wire upstream `record` outputs here, or name library documents. | |
| _files | No | The project: record references shaped like _subject. Their records become library documents a tool names in sequences/parts/document; a trace or alignment is found by file name. | |
| leader | No | leader placed before the FIRST ribosome-binding site (defaults to the design leader). Advanced. | |
| _subject | No | The record to act on: exactly one of sequence, accession (+source), sample (an id from list_samples) or file ({name, text} or {name, base64}); record_index picks one record of several. | |
| promoter | No | promoter sequence to place in front of the operon (optional). Advanced. | |
| terminator | No | terminator sequence to place after the last gene (optional). Advanced. | |
| include_subject | No | put the node's subject first, as the first gene. | |
| target_strength | No | relative initiation strength to aim for at every gene, on the model's own scale — 1 is as strong as its reference site. Overridden per gene by `target_strengths`. | |
| target_strengths | No | per-gene target strengths, aligned to `cds` — the Operon panel gives every row its own, and a run through this door could not say the same thing. Shorter than `cds` falls back to `target_strength` for the rest. Advanced. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| genes | Yes | per gene: the RBS designed for it, its spacing, the strength achieved and whether it hit the target | |
| layout | Yes | every element in order — promoter, each RBS, each CDS, terminator — with its start and end | |
| record | Yes | the assembled operon as a record | |
| onTarget | Yes | true when EVERY gene reached its target strength — the number to check before ordering | |
| sequence | Yes | the assembled operon sequence |