restriction_ligate
Cut and ligate in ONE POT (pydna restriction_ligation_assembly): every input is digested by the same enzymes inside the reaction and the pieces are joined as they appear, so a junction that re-forms a recognition site can be cut again. This is the reaction Golden Gate is a special case of, and it is a different chemistry from ligate_fragments, which digests first and then ligates whatever the digest left. Reports how many sites of the FIRST enzyme each product still carries — a finished construct has none.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| blunt | No | allow blunt-end joins as well as sticky. | |
| _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. | |
| enzymes | No | the enzymes in the pot — used for every input. Left unset, the run uses your active enzyme collection. | |
| _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. | |
| fragments | No | the molecules to put in the pot — wire upstream `record` outputs here, or name library documents. | |
| end_origins | No | what MADE each input's ends, positionally. In a one-pot reaction almost every end is cut INSIDE the tube and is therefore freshly 5'-phosphorylated, so this changes the answer only for an input's own original terminus — reachable only when it arrives already sticky, which today means an annealed oligo adapter. Advanced. | |
| circular_only | No | report only circular products. | |
| end_treatments | No | the phosphatase or kinase applied to each input, positionally. Same reach as `end_origins`: an original sticky terminus only. Advanced. | |
| include_subject | No | also put the node's subject in the pot. | |
| sort_by_recognition_sites | No | sort products by how many sites of the FIRST enzyme they still carry, fewest first — this floats the finished construct to the top. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| layout | Yes | where each piece and join sits ON the product: the spans the map draws | |
| record | Yes | the first product, as a record — with the sort on, the one carrying the fewest remaining sites | |
| products | Yes | every product | |
| junctions | Yes | the junctions formed, with the overhang each was made by — wire into score_overhang_fidelity | |
| productCount | Yes | number of products (>1 = the pieces go together more than one way) | |
| nickedJunctions | Yes | indices of junctions left NICKED by a missing 5'-phosphate on one strand — the product still transforms and is repaired in vivo | |
| recognitionSites | Yes | sites of the FIRST enzyme still in the first product. 0 = finished: the reaction cannot re-cut it | |
| partiallyDigested | Yes | inputs whose products were DROPPED because they would have needed a partial digest — a product that needs the enzyme to skip a site it must have cut is not a bench outcome |