def test_hgnc():
h = HGNC()
h.get_info()
h.fetch('symbol', 'ZNF3')
h.fetch('alias_name', 'A-kinase anchor protein, 350kDa')
h.search('BRAF')
h.search('symbol', 'ZNF*')
h.search('symbol', 'ZNF?')
h.search('symbol', 'ZNF*+AND+status:Approved')
h.search('symbol', 'ZNF3+OR+ZNF12')
h.search('symbol', 'ZNF*+NOT+status:Approved')
def test_hgnc():
h = HGNC()
h.get_info()
h.fetch("symbol", "ZNF3")
h.fetch("alias_name", "A-kinase anchor protein, 350kDa")
h.search("BRAF")
h.search("symbol", "ZNF*")
h.search("symbol", "ZNF?")
h.search("symbol", "ZNF*+AND+status:Approved")
h.search("symbol", "ZNF3+OR+ZNF12")
h.search("symbol", "ZNF*+NOT+status:Approved")
def kegg_to_hugo(genes, species='hsa'):
"""
Converts all KEGG names to HGNC
Parameters
----------
genes : list
species : str
Returns
-------
dict
"""
prefix = species + ':'
hugo = HGNC(verbose=True)
hugo_dict = {}
not_found = set()
for i in genes:
tmp_name = i.lstrip(prefix)
mapping = hugo.search(tmp_name)
if 'response' in mapping:
response = mapping['response']
if 'numFound' in response:
if response['numFound'] == 0:
not_found.add(i)
continue
elif response['numFound'] == 1:
docs = response['docs'][0]
hugo_dict[i] = docs['symbol']
continue
else:
if 'symbol' in response['docs'][0]:
hugo_dict[i] = response['docs'][0]['symbol']
else:
not_found.add(i)
if not_found != 0:
print("{} not found after HGNC mapping".format(len(not_found)))
print("{} ".format(not_found))
return hugo_dict, not_found
def kegg_to_hugo(genes, species='hsa'):
"""
Converts all KEGG names to HGNC
Parameters
----------
genes : list
species : str
Returns
-------
dict
"""
prefix = species + ':'
hugo = HGNC(verbose=True)
hugo_dict = {}
not_found = set()
for i in genes:
tmp_name = i.lstrip(prefix)
mapping = hugo.search(tmp_name)
if 'response' in mapping:
response = mapping['response']
if 'numFound' in response:
if response['numFound'] == 0:
not_found.add(i)
continue
elif response['numFound'] == 1:
docs = response['docs'][0]
hugo_dict[i] = docs['symbol']
continue
else:
if 'symbol' in response['docs'][0]:
hugo_dict[i] = response['docs'][0]['symbol']
else:
not_found.add(i)
if not_found != 0:
print("{} not found after HGNC mapping".format(len(not_found)))
print("{} ".format(not_found))
return hugo_dict, not_found
