def test_build_hgnc_gene_missing_key(test_gene, key):
## GIVEN a dictionary with gene information
# WHEN deleteing key
test_gene.pop(key)
# THEN calling build_hgnc_gene() will raise KeyError
with pytest.raises(KeyError):
build_hgnc_gene(test_gene)
def test_build_hgnc_gene_inappropriate_value(test_gene, key):
## GIVEN a dictionary with gene information
# WHEN setting key to a non-valid value
test_gene[key] = "cause_error"
# THEN calling build_hgnc_gene() will raise ValueError
with pytest.raises(ValueError):
build_hgnc_gene(test_gene)
def test_build_hgnc_gene_inappropriate_type(test_gene, key):
## GIVEN a dictionary with gene information
# WHEN setting key to None
test_gene[key] = None
# THEN calling build_hgnc_gene() will raise TypeError
with pytest.raises(TypeError):
build_hgnc_gene(test_gene)
def gene_bulk(genes):
"""Return a list with HgncGene objects"""
bulk = []
for gene_key in genes:
bulk.append(build_hgnc_gene(genes[gene_key]))
return bulk
def gene_bulk_38(genes):
"""Return a list with HgncGene objects"""
bulk = []
for gene_key in genes:
gene_obj = build_hgnc_gene(genes[gene_key])
gene_obj["build"] = "38"
bulk.append(gene_obj)
return bulk
def test_build_hgnc_genes(genes):
# GIVEN a dictionary with hgnc genes
# WHEN building hgnc gene objecs
for hgnc_id in genes:
gene_info = genes[hgnc_id]
gene_obj = build_hgnc_gene(gene_info)
# THEN check that the gene models have a hgnc id
assert gene_obj["hgnc_id"]
def test_build_hgnc_genes(genes):
# GIVEN a dictionary with hgnc genes
# WHEN building hgnc gene objecs
for hgnc_id in genes:
gene_info = genes[hgnc_id]
gene_obj = build_hgnc_gene(gene_info)
# THEN check that the gene models have a hgnc id
assert gene_obj['hgnc_id']
def test_build_hgnc_gene_no_id():
gene_info = {
"hgnc_symbol": "TEST",
"ensembl_gene_id": "ENSTEST",
"chromosome": "1",
"start": 1,
"end": 1000,
}
with pytest.raises(KeyError):
gene_obj = build_hgnc_gene(gene_info)
def test_build_hgnc_gene_no_id():
gene_info = {
'hgnc_symbol': 'TEST',
'ensembl_gene_id': 'ENSTEST',
'chromosome': '1',
'start': 1,
'end': 1000,
}
with pytest.raises(KeyError):
gene_obj = build_hgnc_gene(gene_info)
def test_build_hgnc_gene_no_id():
gene_info = {
'hgnc_symbol': 'TEST',
'ensembl_gene_id': 'ENSTEST',
'chromosome': '1',
'start': 1,
'end': 1000,
}
with pytest.raises(KeyError):
gene_obj = build_hgnc_gene(gene_info)
def test_build_hgnc_gene():
gene_info = {
"hgnc_id": 100,
"hgnc_symbol": "TEST",
"ensembl_gene_id": "ENSTEST",
"chromosome": "1",
"start": 1,
"end": 1000,
}
gene_obj = build_hgnc_gene(gene_info)
assert gene_obj["hgnc_id"] == gene_info["hgnc_id"]
assert gene_obj["hgnc_symbol"] == gene_info["hgnc_symbol"]
assert gene_obj["length"] == gene_info["end"] - gene_info["start"]
assert gene_obj["ensembl_id"] == gene_info["ensembl_gene_id"]
def test_build_hgnc_gene():
gene_info = {
'hgnc_id': 100,
'hgnc_symbol': 'TEST',
'ensembl_gene_id': 'ENSTEST',
'chromosome': '1',
'start': 1,
'end': 1000,
}
gene_obj = build_hgnc_gene(gene_info)
assert gene_obj['hgnc_id'] == gene_info['hgnc_id']
assert gene_obj['hgnc_symbol'] == gene_info['hgnc_symbol']
assert gene_obj['length'] == gene_info['end'] - gene_info['start']
assert gene_obj['ensembl_id'] == gene_info['ensembl_gene_id']
def test_build_hgnc_gene():
gene_info = {
'hgnc_id': 100,
'hgnc_symbol': 'TEST',
'ensembl_gene_id': 'ENSTEST',
'chromosome': '1',
'start': 1,
'end': 1000,
}
gene_obj = build_hgnc_gene(gene_info)
assert gene_obj['hgnc_id'] == gene_info['hgnc_id']
assert gene_obj['hgnc_symbol'] == gene_info['hgnc_symbol']
assert gene_obj['length'] == gene_info['end'] - gene_info['start']
assert gene_obj['ensembl_id'] == gene_info['ensembl_gene_id']
