def test_update_transcripts_information(hgnc_gene, variant_gene):
## GIVEN a hgnc gene, a variant gene and a variant object
variant_obj = {}
assert "primary_transcripts" not in variant_gene
## WHEN updating the transcript information for the variant gene
update_transcripts_information(variant_gene, hgnc_gene, variant_obj)
## THEN assert the function has completed without errors
assert "primary_transcripts" in variant_gene
def test_update_transcripts_information_refseq_id(variant_gene, hgnc_gene):
## GIVEN a variants gene with no primary transcript
variant_obj = {}
## WHEN updating the transcripts information
update_transcripts_information(variant_gene, hgnc_gene, variant_obj, genome_build=None)
## THEN assert that the tx on variant gene has been given a ref seq id
assert variant_gene["transcripts"][0].get("refseq_id") == "NM_001193301"
## THEN assert that the variant obj has refseq ids
assert variant_obj["has_refseq"] is True
def test_update_transcripts_information_is_primary(variant_gene, hgnc_gene):
## GIVEN a variants gene with no primary transcript
assert variant_gene["transcripts"][0].get("is_primary") is None
variant_obj = {}
## WHEN updating the transcripts information
update_transcripts_information(variant_gene, hgnc_gene, variant_obj, genome_build=None)
## THEN assert that the tx on variant gene has been labeled primary transcript
assert variant_gene["transcripts"][0].get("is_primary") is True
def test_update_transcripts_information_disease_associated(variant_gene, hgnc_gene):
## GIVEN a variants gene with info about disease associated tx
assert variant_gene["transcripts"][0].get("is_disease_associated") is None
variant_obj = {}
variant_gene["disease_associated_no_version"] = ["NM_022089"]
## WHEN updating the transcripts information
update_transcripts_information(variant_gene, hgnc_gene, variant_obj, genome_build=None)
## THEN assert that the tx on variant gene has is disease associated
assert variant_gene["transcripts"][0].get("is_disease_associated") is True
def test_update_transcripts_information_disease_associated():
## GIVEN a variants gene with info about disease associated tx
variant_gene = {
"hgnc_id":
10729,
"hgnc_symbol":
"SEMA4A",
"disease_associated_no_version": ["NM_001193301"],
"transcripts": [{
"transcript_id": "ENST00000355014",
"hgnc_id": 10729,
"protein_id": "ENSP00000347117",
"sift_prediction": "unknown",
"polyphen_prediction": "unknown",
"swiss_prot": "Q9H3S1",
"biotype": "protein_coding",
"functional_annotations": ["intron_variant"],
"region_annotations": ["intronic"],
"intron": "10/14",
"strand": "+",
"coding_sequence_name": "c.1135-4554G>A",
"is_canonical": False,
}],
}
assert variant_gene["transcripts"][0].get("is_disease_associated") is None
hgnc_gene = {
"_id": {
"$oid": "5c8112e701f54818d3cbc04a"
},
"hgnc_id":
10729,
"hgnc_symbol":
"SEMA4A",
"ensembl_id":
"ENSG00000196189",
"chromosome":
"1",
"start":
156117157,
"end":
156147543,
"length":
30386,
"description":
"semaphorin 4A",
"aliases": ["SEMA4A", "SEMAB", "CORD10", "SemB", "FLJ12287"],
"primary_transcripts": ["NM_022367"],
"inheritance_models": ["AD", "AR"],
"entrez_id":
64218,
"omim_id":
607292,
"ucsc_id":
"uc001fnl.4",
"uniprot_ids": ["Q9H3S1"],
"vega_id":
"OTTHUMG00000014042",
"pli_score":
0.615371620982326,
"incomplete_penetrance":
False,
"build":
"37",
"transcripts": [{
"_id": {
"$oid": "5c81130601f54818d3cc0514"
},
"ensembl_transcript_id": "ENST00000355014",
"hgnc_id": 10729,
"chrom": "1",
"start": 156119810,
"end": 156147535,
"is_primary": True,
"refseq_id": "NM_001193301",
"refseq_identifiers": ["NM_001193301"],
"build": "37",
"length": 27725,
}],
}
variant_obj = {}
## WHEN updating the transcripts information
update_transcripts_information(variant_gene,
hgnc_gene,
variant_obj,
genome_build=None)
## THEN assert that the tx on variant gene has is disease associated
assert variant_gene["transcripts"][0].get("is_disease_associated") is True