assemble_multiple_inserts
Open ONE circular backbone at several places and place several inserts in a single step. A complete digest at n sites leaves n arcs and n gaps between them, and every gap has to be filled for the ring to close; the arcs and the inserts go to the same homology assembler the single-insert tool uses, and which insert lands in which gap is read off each construct the homology graph closes rather than guessed. It designs no homology arm: an insert arrives with the ends it has, and a set whose ends do not meet the arcs is the assembler's own refusal.
Input Schema
| Name | Required | Description | Default |
|---|---|---|---|
| _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 | Yes | the enzymes that open the backbone, by name (1409 in the cloning catalogue). Their sites ARE the insertion points, so two single-cutters give two of them; a name the catalogue does not carry is refused by name rather than ignored. | |
| inserts | Yes | the fragments to place, one per insertion point — wire upstream `record` outputs here, or name library documents. | |
| _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. | |
| backbone | No | the circular vector to open. Leave unset to use the open record. | |
| max_constructs | No | cap on how many distinct constructs are enumerated. Advanced. | |
| max_homology_bp | No | longest terminal homology considered; the bound is EXCLUSIVE, as upstream's own range is. In bp. | |
| min_homology_bp | No | minimum terminal homology for two ends to join. In bp. |
Output Schema
| Name | Required | Description | Default |
|---|---|---|---|
| arcs | Yes | the backbone's arcs: their lengths and the enzyme that made each end — the insertion points, made readable | |
| record | Yes | the first construct, as a record | |
| reading | Yes | what was planned, generated from the enumeration rather than the request | |
| cutCounts | Yes | sites found per enzyme, so an enzyme that does not cut is named rather than silently absent | |
| placements | Yes | every construct the ring closes on, each with the inserts in the order they sit around it | |
| insertionPoints | Yes | how many gaps the digest left, which is how many inserts the step takes |