def generate_genemap2(genes, api_key):
"""Generate a reduced file with omim genemap2 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, genemap2=True)
genemap2_lines = mim_files['genemap2']
# Yield the header lines
for line in genemap2_lines:
if line.startswith('#'):
yield line
else:
break
for gene_info in parse_genemap2(genemap2_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_genemap_file(genemap_handle):
# WHEN parsing a valid genemap handle
i = 0
for i, res in enumerate(parse_genemap2(genemap_handle)):
assert "mim_number" in res
# THEN items are returned
assert i > 0
def generate_genemap2(genes, api_key):
"""Generate a reduced file with omim genemap2 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, genemap2=True)
genemap2_lines = mim_files['genemap2']
# Yield the header lines
for line in genemap2_lines:
if line.startswith('#'):
yield line
else:
break
for gene_info in parse_genemap2(genemap2_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_genemap():
for res in parse_genemap2(GENEMAP_LINES):
assert res['Chromosome'] == 'chr1'
assert res['mim_number'] == 615291
assert res['hgnc_symbol'] == 'B3GALT6'
assert res['inheritance'] == set(['AR'])
for phenotype in res['phenotypes']:
assert phenotype['mim_number']
assert phenotype['inheritance']
def test_parse_genemap(genemap_lines):
for res in parse_genemap2(genemap_lines):
assert res["Chromosome"] == "chr1"
assert res["mim_number"] == 615291
assert res["hgnc_symbol"] == "B3GALT6"
assert res["inheritance"] == set(["AR"])
for phenotype in res["phenotypes"]:
assert phenotype["mim_number"]
assert phenotype["inheritance"]
def test_parse_genemap():
for res in parse_genemap2(GENEMAP_LINES):
assert res['Chromosome'] == 'chr1'
assert res['mim_number'] == 615291
assert res['hgnc_symbol'] == 'B3GALT6'
assert res['inheritance'] == set(['AR'])
for phenotype in res['phenotypes']:
assert phenotype['mim_number']
assert phenotype['inheritance']
def test_parse_genemap_file(genemap_handle):
for i, res in enumerate(parse_genemap2(genemap_handle)):
assert 'mim_number' in res
assert i > 0
def test_parse_genemap_file(genemap_handle):
for i,res in enumerate(parse_genemap2(genemap_handle)):
assert 'mim_number' in res
assert i > 0