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Merge branch 'issue-95-take2' of https://github.com/cancervariants/fusor
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katiestahl committed Jul 22, 2024
2 parents 74db34c + a3e67d1 commit 9cd280c
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Showing 2 changed files with 7 additions and 10 deletions.
2 changes: 1 addition & 1 deletion src/fusor/fusor.py
Original file line number Diff line number Diff line change
Expand Up @@ -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
"""
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15 changes: 6 additions & 9 deletions src/fusor/models.py
Original file line number Diff line number Diff line change
Expand Up @@ -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",
Expand Down Expand Up @@ -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": {
Expand All @@ -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": {
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