Annotations schema updates #1281
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| Original file line number | Diff line number | Diff line change |
|---|---|---|
| @@ -1,34 +1,90 @@ | ||
| { | ||
| "type" : "object", | ||
| "$schema": "http://json-schema.org/draft-06/schema#", | ||
| "$id": "https://nextstrain.org/schemas/augur/annotations", | ||
| "title": "Schema for the 'annotations' property (node-data JSON) or the 'genome_annotations' property (auspice JSON)", | ||
| "properties": { | ||
| "nuc": { | ||
| "type": "object", | ||
| "allOf": [{ "$ref": "#/$defs/startend" }], | ||
| "properties": { | ||
| "start": { | ||
| "enum": [1], | ||
| "$comment": "nuc must begin at 1" | ||
| }, | ||
| "strand": { | ||
| "type": "string", | ||
| "enum":["+"], | ||
| "description": "Strand is optional for nuc, as it should be +ve for all genomes (-ve strand genomes are reverse complemented)", | ||
| "$comment": "Auspice will not proceed if the JSON has strand='-'" | ||
| } | ||
| }, | ||
| "additionalProperties": true, | ||
| "$comment": "All other properties are unused by Auspice." | ||
| } | ||
| }, | ||
| "required": ["nuc"], | ||
| "patternProperties": { | ||
| "^(?!nuc)[a-zA-Z0-9*_-]+$": { | ||
| "$comment": "Each object here defines a single CDS", | ||
| "type": "object", | ||
| "oneOf": [{ "$ref": "#/$defs/startend" }, { "$ref": "#/$defs/segments" }], | ||
| "additionalProperties": true, | ||
| "required": ["strand"], | ||
| "properties": { | ||
| "gene": { | ||
| "type": "string", | ||
| "description": "The name of the gene the CDS is from. Optional.", | ||
| "$comment": "Shown in on-hover infobox & influences default CDS colors" | ||
| }, | ||
| "strand": { | ||
| "description": "Strand of the CDS", | ||
| "type": "string", | ||
| "enum": ["-", "+"] | ||
| }, | ||
| "color": { | ||
| "type": "string", | ||
| "description": "A CSS color or a color hex code. Optional." | ||
| }, | ||
| "display_name": { | ||
| "type": "string", | ||
| "$comment": "Shown in the on-hover info box" | ||
| }, | ||
| "description": { | ||
| "type": "string", | ||
|
There was a problem hiding this comment. Suggestion: Add Even though Auspice only cares if the value is I started this in #1279 but that PR can be closed and the change included in here. There was a problem hiding this comment. Thanks for the review -- really appreciated! We're going to have to think through this. All annotations are interpreted by Auspice as CDSs, so a strand of I can allow them in the schema and then have Auspice filter to Update: Auspice PR now ignores any non-nuc annotation which is not explicitly +/- strand There was a problem hiding this comment. Have shifted this conversation to #1279 |
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| "$comment": "Shown in the on-hover info box" | ||
| } | ||
| } | ||
| } | ||
| }, | ||
| "$defs": { | ||
| "startend": { | ||
| "type": "object", | ||
| "required": ["start", "end"], | ||
| "properties": { | ||
| "start": { | ||
| "type": "integer", | ||
| "minimum": 1, | ||
| "description": "Start position (one-based, following GFF format)" | ||
| }, | ||
| "end": { | ||
| "type": "integer", | ||
| "minimum": 2, | ||
| "description": "End position (one-based, following GFF format). This value _must_ be greater than the start." | ||
| } | ||
| } | ||
| }, | ||
| "segments": { | ||
| "type": "object", | ||
| "required": ["segments"], | ||
| "properties": { | ||
| "segments": { | ||
| "type": "array", | ||
| "minItems": 1, | ||
| "items": { | ||
| "type": "object", | ||
| "allOf": [{ "$ref": "#/$defs/startend" }] | ||
| } | ||
| } | ||
| } | ||
| } | ||
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Late to the party, but shouldn't we in principle allow each cds fragment to have its own strandedness? Here the strand is fixed for all fragments, which will be fine in most cases but who knows, maybe sometimes fragments might come from opposite strands?
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ChatGPT tells me that strandedness never changes within a CDS so then what we have here should work in all cases.
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With trans-splicing it might work, but doesn't seem to happen in viruses so we should be good for now: https://en.wikipedia.org/wiki/Trans-splicing