def generate_mim2genes(genes, api_key):
"""Generate a reduced file with omim mim2gene information
Args:
genes(dict): A dictionary with hgnc_symbol as key and hgnc_id as value
api_key(str)
Yields:
print_line(str): Lines from the reduced file
"""
mim_files = fetch_mim_files(api_key, mim2genes=True)
mim2gene_lines = mim_files['mim2genes']
for line in mim2gene_lines:
if line.startswith('#'):
yield line
else:
break
for gene_info in parse_mim2gene(mim2gene_lines):
hgnc_symbol = gene_info.get('hgnc_symbol')
if not hgnc_symbol:
continue
if hgnc_symbol in genes:
yield gene_info['raw']
def generate_mim2genes(genes, api_key):
"""Generate a reduced file with omim mim2gene information
Args:
genes(dict): A dictionary with hgnc_symbol as key and hgnc_id as value
api_key(str)
Yields:
print_line(str): Lines from the reduced file
"""
mim_files = fetch_mim_files(api_key, mim2genes=True)
mim2gene_lines = mim_files['mim2genes']
for line in mim2gene_lines:
if line.startswith('#'):
yield line
else:
break
for gene_info in parse_mim2gene(mim2gene_lines):
hgnc_symbol = gene_info.get('hgnc_symbol')
if not hgnc_symbol:
continue
if hgnc_symbol in genes:
yield gene_info['raw']
def test_parse_mim2gene():
## GIVEN some lines from a mim2gene file
mim2gene_info = parse_mim2gene(MIM2GENE_LINES)
## WHEN parsing the lines
first_entry = next(mim2gene_info)
## ASSERT that they are correctly parsed
# First entry is a gene so it should have a hgnc symbol
assert first_entry['mim_number'] == 615291
assert first_entry['entry_type'] == 'gene'
assert first_entry['hgnc_symbol'] == 'B3GALT6'
def test_parse_mim2gene(mim2gene_lines):
## GIVEN some lines from a mim2gene file
mim2gene_info = parse_mim2gene(mim2gene_lines)
## WHEN parsing the lines
first_entry = next(mim2gene_info)
## ASSERT that they are correctly parsed
# First entry is a gene so it should have a hgnc symbol
assert first_entry["mim_number"] == 615291
assert first_entry["entry_type"] == "gene"
assert first_entry["hgnc_symbol"] == "B3GALT6"
def test_parse_mim2gene():
## GIVEN some lines from a mim2gene file
mim2gene_info = parse_mim2gene(MIM2GENE_LINES)
## WHEN parsing the lines
first_entry = next(mim2gene_info)
## ASSERT that they are correctly parsed
# First entry is a gene so it should have a hgnc symbol
assert first_entry['mim_number'] == 615291
assert first_entry['entry_type'] == 'gene'
assert first_entry['hgnc_symbol'] == 'B3GALT6'
def test_parse_mim2gene_file(mim2gene_handle):
# Just check that the file exists and that some result is given
for i, res in enumerate(parse_mim2gene(mim2gene_handle)):
assert 'mim_number' in res
assert i > 0
def test_parse_mim2gene_file(mim2gene_handle):
# Just check that the file exists and that some result is given
for i,res in enumerate(parse_mim2gene(mim2gene_handle)):
assert 'mim_number' in res
assert i > 0
