auto_annotate
Find and name known features on the subject — vector parts, origins, resistance markers and tags — by exact match, by local alignment (which finds a diverged copy and reports the identity and coverage that earned it), or by both, on either strand and across the origin, plus Cre/loxP and Gateway att recognition sites. Emits an annotated record, so a downstream map or export carries the annotations.
Input Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| mode | No | how to match a library entry: "exact" finds only a sequence spelled byte for byte, "alignment" finds a diverged copy and reports its identity and coverage, "both" runs each and keeps what only the other found. | both |
| lox_p | No | detect Cre/loxP-family recognition sites. | |
| _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. | |
| policy | No | what the emitted record does with the features it already had: `merge` keeps them all and skips a hit already there to the base, `overwrite` replaces a same-strand feature a hit overlaps, `clear` drops every existing feature first. | merge |
| gateway | No | detect Gateway att recombination sites. | |
| _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. | |
| libraries | No | which feature corpora to search, by id (an id from annotation-library/manifest.json, or "legacy" for the unsourced set). Empty means all of them. | |
| max_expect | No | protein corpora only: the E-value a translated (six-frame) match must beat to be reported. It also sets the score the search runs at, so a stricter cutoff is a faster scan. Advanced. | |
| alternatives | No | protein corpora only: how many runners-up to keep on each call, so a near relative is reported rather than implied. Advanced. | |
| genetic_code | No | protein corpora only: the NCBI translation table the six frames are read under. 1 is the standard code. Advanced. | |
| min_coverage | No | protein corpora only: drop a translated call covering less than this much of the database protein's own length. Advanced. | |
| min_identity | No | protein corpora only: drop a translated call under this percent identity over the residues aligned. Advanced. | |
| accepted_only | No | keep only hits clearing the corpus authority's own acceptance policy (>=95% identity, with a coverage bar that depends on the feature's length). Also decides overlaps: a hit the authority would reject cannot displace one it would accept. Only applies when mode is alignment or both. Advanced. | |
| greedy_gateway | No | permissive att core matching — finds more sites, including partial ones. Only applies when gateway is true. Advanced. | |
| hide_fragments | No | hide hits covering under 95% of their database entry, which upstream calls fragments. Only applies when mode is alignment or both. Advanced. | |
| min_pi_per_match | No | lowest identity-weighted coverage worth reporting; upstream's own floor is 3, below which a hit is a fragment of a composite feature rather than the feature. Only applies when mode is alignment or both. Advanced. |
Output Schema
TableJSON Schema
| Name | Required | Description | Default |
|---|---|---|---|
| record | Yes | the subject with the found features added | |
| features | Yes | every feature found, with its source detector | |
| perSource | Yes | hit count per detector | |
| featureCount | Yes | how many features were found |