Add JSON schema for STRchive-loci.json

[hdashnow]

For #94

I've got some basic validation set up. Let me know what else would be useful. Maybe an option to create a new blank locus to make it easier to add new loci to the JSON?

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[Copilot]

Pull Request Overview

This PR adds a JSON schema for STRchive-loci and introduces a new validation script along with dependency management updates. Key changes include:

• Addition of scripts/validate-loci.py to provide JSON schema validation.
• Updates to environment YML files to include the jsonschema dependency.
• Minor modifications to scripts/check-loci.py for data cleanup improvements.

Reviewed Changes

Copilot reviewed 5 out of 7 changed files in this pull request and generated 1 comment.

File	Description
scripts/validate-loci.py	Adds a JSON schema validation script for STRchive loci JSON data.
scripts/setup-miniconda-patched-environment.yml	Updates environment dependencies to include jsonschema.
scripts/environment.yml	Updates environment dependencies to include jsonschema.
scripts/check-loci.py	Adjusts list field transformations and updates logging output.

Files not reviewed (2)

• data/STRchive-loci.json: Language not supported
• workflow/Snakefile: Language not supported

Comments suppressed due to low confidence (1)

scripts/check-loci.py:211

• The f-string here has conflicting single quotes when accessing the 'id' key. Consider changing the outer string to use double quotes or the inner key to use alternate quoting (e.g., {record["id"]}).

sys.stderr.write(f'Updating {record['id']} {field} from {old} to {record[field]}\n')

[Macayla-weiner]

I think a blank locus would be useful. I have been using this (as you have it now) to begin adding PLIN4 and have no complaints!

Edit: maybe possible tags would be good to add too -- it took me some looking to figure out what tags I needed to put on PLIN4.

[laurelhiatt]

I like the schema, I like the examples. beautiful

[hdashnow]

I think a blank locus would be useful. I have been using this (as you have it now) to begin adding PLIN4 and have no complaints!

Edit: maybe possible tags would be good to add too -- it took me some looking to figure out what tags I needed to put on PLIN4.

@Macayla-weiner I added some more tag examples. Let me know what you think. Are there other's you'd suggest including?

 "locus_tags": {
        "description": "Tags for the locus, used for grouping similar loci and for flagging loci with specific characteristics",
        "examples": [ "somatic_instability", "contraction", "anticipation", "conflicting_evidence", "sparse_evidence", "maternal_expansion", "length_affects_penetrance", "length_affects_severity", "length_affects_onset" ],
        "type": "array",
        "items": {
          "type": [ "string", "null" ]
        }
      },
      "disease_tags": {
        "description": "Tags for the disease, used for grouping similar diseases",
        "examples": [ "ataxia" ],
        "type": "array",
        "items": {
          "type": [ "string", "null" ]
        }

[Toromtomtom]

Thanks for adding the schema! I suggest adding that the genomic coordinates are 1-based rather than 0-based. The wording is adopted from the VCF specification.

[Toromtomtom]

Suggested change

	"description": "Start position in hg38 reference genome",
	"description": "Start position in hg38 reference genome, with the 1st base having position 1",

[Toromtomtom]

Suggested change

	"description": "Stop position in hg38 reference genome",
	"description": "Stop position in hg38 reference genome, with the 1st base having position 1",

[Toromtomtom]

Suggested change

	"description": "Start position in hg19 reference genome",
	"description": "Start position in hg19 reference genome, with the 1st base having position 1",

[Toromtomtom]

Suggested change

	"description": "Stop position in hg19 reference genome",
	"description": "Stop position in hg19 reference genome, with the 1st base having position 1",

[Toromtomtom]

Suggested change

	"description": "Start position in chm13-T2T reference genome",
	"description": "Start position in chm13-T2T reference genome, with the 1st base having position 1",

[Toromtomtom]

Suggested change

	"description": "Stop position in chm13-T2T reference genome",
	"description": "Stop position in chm13-T2T reference genome, with the 1st base having position 1",

[hdashnow]

Possible additional changes:

• Suggest combining locus_structure and flank_motif
• Remove mechanism source

[hdashnow]

Thanks for adding the schema! I suggest adding that the genomic coordinates are 1-based rather than 0-based. The wording is adopted from the VCF specification.

@Toromtomtom this is a critical point! These raw values should be bed-style 0-based. They get converted to 1-based for some applications, for example, when creating the UCSC links. I'll make this explicit.

[hdashnow]

I think this is good to go. I'll leave it hanging for another 24 hours in case there are additional suggestions.

Note, this reflects the state of the STRchive json format today. There are some planned breaking changes that will be introduced in a future PR.