diff --git a/src/fusor/fusor.py b/src/fusor/fusor.py index 6fb16fe..c3d28ce 100644 --- a/src/fusor/fusor.py +++ b/src/fusor/fusor.py @@ -322,7 +322,7 @@ def gene_element( :param str gene: Gene :param bool use_minimal_gene: `True` if minimal gene object - (`id`, `gene_id`, `label`) will be used. `False` if + (`id` and `label`) will be used. `False` if gene-normalizer's gene object will be used :return: GeneElement, warning """ diff --git a/src/fusor/models.py b/src/fusor/models.py index 930c6d9..6088f6e 100644 --- a/src/fusor/models.py +++ b/src/fusor/models.py @@ -73,18 +73,17 @@ class FunctionalDomain(BaseModel): "label": "Tyrosine-protein kinase, catalytic domain", "id": "interpro:IPR020635", "associatedGene": { - "id": "gene:NTRK1", - "gene_id": "hgnc:8031", - "label": "8031", + "id": "hgnc:8031", + "label": "NTRK1", "type": "Gene", }, "sequenceLocation": { - "id": "SL.vJvm06Wl5J7DXHynR9ksW7IK3_3jlFK6", + "id": "ga4gh:SL.vJvm06Wl5J7DXHynR9ksW7IK3_3jlFK6", "start": 510, "end": "781", "type": "SequenceLocation", "sequenceReference": { - "id": "NP_002520.2", + "id": "NC_000022.11", "label": "GRCh38:chr22", "type": "SequenceReference", "refgetAccession": "SQ.7B7SHsmchAR0dFcDCuSFjJAo7tX87krQ", @@ -172,8 +171,7 @@ def check_exons(cls, values): "label": "TPM3", }, "elementGenomicStart": { - # TODO: this digest may not be correct, but putting a placeholder example here for now - "id": "SL.vJvm06Wl5J7DXHynR9ksW7IK3_3jlFK6", + "id": "ga4gh:SL.2K1vML0ofuYrYncrzzXUQOISRFJldZrO", "type": "SequenceLocation", "label": "NC_000001.11", "sequenceReference": { @@ -184,8 +182,7 @@ def check_exons(cls, values): "end": 154192136, }, "elementGenomicEnd": { - # TODO: this digest may not be correct, but putting a placeholder example here for now - "id": "SL.vJvm06Wl5J7DXHynR9ksW7IK3_3jlFK6", + "id": "ga4gh:SL.rtR6x2NnJEpROlxiT_DY9C-spf6ijYQi", "type": "SequenceLocation", "label": "NC_000001.11", "sequenceReference": {