def test_parse_gene():
## GIVEN gene line and header
header = [
"hgnc_id",
"hgnc_symbol",
"disease_associated_transcripts",
"reduced_penetrance",
"genetic_disease_models",
"mosaicism",
"database_entry_version",
]
hgnc_id = "10"
hgnc_symbol = "hello"
transcripts = "a,b,c"
penetrance = "YES"
models = "AR,AD"
mosaicism = ""
version = ""
gene_line = [
hgnc_id,
hgnc_symbol,
transcripts,
penetrance,
models,
mosaicism,
version,
]
gene_info = dict(zip(header, gene_line))
## WHEN parsing the genes
gene = parse_gene(gene_info)
## THEN assert that the gene is correctly parsed
assert gene["hgnc_id"] == int(hgnc_id)
assert gene["hgnc_symbol"] == hgnc_symbol
assert gene["transcripts"] == transcripts.split(",")
assert gene["inheritance_models"] == models.split(",")
assert gene["reduced_penetrance"] is True if penetrance else False
assert gene["mosaicism"] is False
assert gene["database_entry_version"] == version
## WHEN alternative transcript index name
gene_info.pop("disease_associated_transcripts")
gene_info["disease_associated_transcript"] = transcripts
## THEN transcript asserts same
gene = parse_gene(gene_info)
assert gene["transcripts"] == transcripts.split(",")
## WHEN alternative transcript index name
gene_info.pop("disease_associated_transcript")
gene_info["transcripts"] = transcripts
## THEN transcript asserts same
gene = parse_gene(gene_info)
assert gene["transcripts"] == transcripts.split(",")
def test_parse_gene():
## GIVEN gene line and header
header = [
"hgnc_id", "hgnc_symbol", "disease_associated_transcripts",
"reduced_penetrance", "genetic_disease_models", "mosaicism",
"database_entry_version"
]
hgnc_id = '10'
hgnc_symbol = 'hello'
transcripts = 'a,b,c'
penetrance = 'YES'
models = 'AR,AD'
mosaicism = ''
version = ''
gene_line = [
hgnc_id, hgnc_symbol, transcripts, penetrance, models, mosaicism,
version
]
## WHEN parsing the genes
gene = parse_gene(gene_line, header)
## THEN assert that the gene is correctly parsed
assert gene['hgnc_id'] == int(hgnc_id)
assert gene['hgnc_symbol'] == hgnc_symbol.upper()
assert gene['transcripts'] == transcripts.split(',')
assert gene['inheritance_models'] == models.split(',')
assert gene['reduced_penetrance'] == True if penetrance else False
assert gene['mosaicism'] == False
assert gene['database_entry_version'] == version
def test_parse_minimal_gene():
## GIVEN minimal gene line and header
header = ["hgnc_id"]
gene_line = ["10"]
## WHEN parsing the genes
gene = parse_gene(gene_line, header)
## THEN assert that the gene is correctly parsed
assert gene['hgnc_id'] == 10
def test_parse_minimal_gene():
## GIVEN minimal gene line and header
header = ["hgnc_id"]
gene_line = ["10"]
gene_info = dict(zip(header, gene_line))
## WHEN parsing the genes
gene = parse_gene(gene_info)
## THEN assert that the gene is correctly parsed
assert gene["hgnc_id"] == 10
def test_parse_minimal_gene():
## GIVEN minimal gene line and header
header = ["hgnc_id"]
gene_line = ["10"]
gene_info = dict(zip(header, gene_line))
## WHEN parsing the genes
gene = parse_gene(gene_info)
## THEN assert that the gene is correctly parsed
assert gene['hgnc_id'] == 10
def test_parse_gene():
## GIVEN gene line and header
header = [
"hgnc_id",
"hgnc_symbol",
"disease_associated_transcripts",
"reduced_penetrance",
"genetic_disease_models",
"mosaicism",
"database_entry_version"
]
hgnc_id = '10'
hgnc_symbol = 'hello'
transcripts = 'a,b,c'
penetrance = 'YES'
models = 'AR,AD'
mosaicism = ''
version = ''
gene_line = [
hgnc_id,
hgnc_symbol,
transcripts,
penetrance,
models,
mosaicism,
version
]
gene_info = dict(zip(header, gene_line))
## WHEN parsing the genes
gene = parse_gene(gene_info)
## THEN assert that the gene is correctly parsed
assert gene['hgnc_id'] == int(hgnc_id)
assert gene['hgnc_symbol'] == hgnc_symbol
assert gene['transcripts'] == transcripts.split(',')
assert gene['inheritance_models'] == models.split(',')
assert gene['reduced_penetrance'] == True if penetrance else False
assert gene['mosaicism'] == False
assert gene['database_entry_version'] == version