DNA Trait assessments

ℹ️

We assume that you completed second tutorial Providing genetic files and that you have:
- Access token stored in ACCESS_TOKEN environment variable
- Created Sample object and stored sample ID in SAMPLE_ID environment variable
- Created Genotype with valid genetic file

Notes:

{ACCESS_TOKEN} must be obtained from the authentication endpoint. See Auth docs for examples.
Before reading trait assessments, Sample object with genetic data must be created. See Basic Sample Setup.

Waiting for DNA Trait Assessments

DNA Trait Assessments will be available once the Genotype analysis is succefuly completed. Genotype analysis is an asynchronous process that is initiated automatically after genotype is created and PBS object identified by genotype's source_uri property becomes available. That means that the API client doesn't initiate processing explicitly and API client is not blockeduntil the file processing is finished.

Client needs to check genotype state by invoking Get Genotype operation.

Once file processing is completed, genotype state will transition to processed:

{
  "id": "312235f8-...-c8b71648471d",
  "assembly": "grch37",
  "source_uri": "string",
  "source_blob_metadata": null,
  "state": "processed",
  ...
}

Reading Trait Assessments

Trait assessments can be fetched by invoking List DNA Traits

All trait assessments can be fetched with a single request:

curl --request GET \
  --url "https://se1.lifenome.com/platform-api/api/core-api/samples/${SAMPLE_ID}/traits/" \
  --header "Content-Type: application/json" \
  --header "Authorization: Bearer ${ACCESS_TOKEN}"

Response will contain paginated list of trait assessment objects:

{
	"count": 179,
	"next": "https://se1.lifenome.com/platform-api/api/samples-api/samples/{SAMPLE_ID}/traits/?limit=50&offset=50",
	"previous": null,
	"results": [
		{
			"trait_code": "achilles-tendinopathy",
			"trait": {
				"code": "achilles-tendinopathy",
				"name": "Achilles Tendinopathy",
				"description": null
			},
			"assessment": {
				"score": 2.5,
				"level": 2,
				"percentile": 95.0
			},
			"coverage": {
				"lookup_snps": 8,
				"snps_found": 6,
				"inhibiting_snps": 1,
				"contributing_snps": 5
			},
			"recommendations": [],
			"axengine": {
				"engine": "default",
				"module": "lfn-wellness-grch37"
			}
		},
		"_comment": "skipped..."
	]
}

Also, single trait assessment can be retrieved by providing TRAIT_CODE in the URL:

curl --request GET \
  --url "https://se1.lifenome.com/platform-api/api/core-api/samples/${SAMPLE_ID}/traits/${TRAIT_CODE}/" \
  --header "Content-Type: application/json" \
  --header "Authorization: Bearer ${ACCESS_TOKEN}"

For example, when TRAIT_CODE="achilles-tendinopathy", response is:

{
 "trait_code": "achilles-tendinopathy",
 "trait": {
	 "code": "achilles-tendinopathy",
	 "name": "Achilles Tendinopathy",
	 "description": null
 },
 "assessment": {
	 "score": 2.5,
	 "level": 2,
	 "percentile": 95.0
 },
 "coverage": {
	 "lookup_snps": 8,
	 "snps_found": 6,
	 "inhibiting_snps": 1,
	 "contributing_snps": 5
 },
 "recommendations": [],
 "axengine": {
	 "engine": "default",
	 "module": "lfn-wellness-grch37"
 }
}