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Annotations schema updates #1281

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Merged
merged 3 commits into from
Aug 20, 2023
Merged

Annotations schema updates #1281

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d6246ca
Update annotations schema to be correct
jameshadfield Aug 16, 2023
37f63b4
[validate] allow local $refs
jameshadfield Aug 16, 2023
c530539
Extend annotations schema
jameshadfield Aug 16, 2023
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50 changes: 30 additions & 20 deletions augur/data/schema-annotations.json
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Original file line number Diff line number Diff line change
@@ -1,34 +1,44 @@
{
"type" : "object",
"$schema": "http://json-schema.org/draft-06/schema#",
"title": "JSON object for the `annotations` key, typically produced by `augur translate`",
"description": "Coordinates etc of genes / genome",
"title": "Schema for the 'annotations' property (node-data JSON) or the 'genome_annotations' property (auspice JSON)",
"properties": {
"nuc": {
"type": "object",
"allOf": [{ "$ref": "#/$defs/startend" }],
"additionalProperties": true,
"$comment": "All other properties are unused by Auspice. Strand is always considered to be positive."
}
},
"required": ["nuc"],
"patternProperties": {
"^[a-zA-Z0-9*_-]+$": {
"type": "object",
"allOf": [{ "$ref": "#/$defs/startend" }],
"additionalProperties": true,
"properties": {
"seqid":{
"description": "Sequence on which the coordinates below are valid. Could be viral segment, bacterial contig, etc",
"$comment": "Unused by Auspice 2.0",
"type": "string"
},
"type": {
"description": "Type of the feature. could be mRNA, CDS, or similar",
"$comment": "Unused by Auspice 2.0",
"strand": {
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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

"description": "Is the gene on the positive ('+') or negative ('-') strand.",
"$comment": "Auspice assumes positive strand unless strand is '-'",
"type": "string"
},
}
}
}
},
"$defs": {
"startend": {
"type": "object",
"required": ["start", "end"],
"properties": {
"start": {
"description": "Gene start position (one-based, following GFF format)",
"type": "number"
"type": "integer",
"minimum": 1,
"description": "Start position (one-based, following GFF format)"
},
"end": {
"description": "Gene end position (one-based closed, last position of feature, following GFF format)",
"type": "number"
},
"strand": {
"description": "Positive or negative strand",
"type": "string",
"enum": ["-","+"]
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Suggestion: Add enum back with additional values.

Even though Auspice only cares if the value is '-' or not, Augur can also export values '?' and None as suggested and implemented in 31f0b26. Defining the possible values here will improve the effectiveness of validation.

I started this in #1279 but that PR can be closed and the change included in here.

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@jameshadfield jameshadfield Aug 17, 2023 •
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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 "?" or "." (which we represent as None) doesn't make sense as a CDS - neither for Auspice to display nor for Augur to translate.

I can allow them in the schema and then have Auspice filter to ["+", "-"], which is probably the most technically correct, but I would think that happily translating "?" / "." features is questionable. For augur translate + GenBank annotations, only CDS features are read and (I believe) it's not possible to encode a CDS in GenBank that's not +/-. I'm not sure what we do for augur translate + GFF annotation.

Update: Auspice PR now ignores any non-nuc annotation which is not explicitly +/- strand

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Have shifted this conversation to #1279

"type": "integer",
"minimum": 2,
"description": "End position (one-based, following GFF format). This value _must_ be greater than the start."
}
}
}
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2 changes: 1 addition & 1 deletion tests/util_support/test_node_data_file.py
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Expand Up @@ -38,7 +38,7 @@ def test_validate_valid(self, build_node_data_file):
build_node_data_file(
f"""
{{
"annotations": {{ "a": {{ "start": 5 }} }},
"annotations": {{ "nuc": {{ "start": 1, "end": 100 }} }},
"generated_by": {{ "program": "augur", "version": "{__version__}" }},
"nodes": {{ "a": 5 }}
}}
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