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 _lookup_hgnc_id(self):
hgnc_web = HGNC()
hgnc = hgnc_web.fetch('hgnc_id', self.external_id)
if hgnc['response']['numFound'] == 1:
self.name = hgnc['response']['docs'][0]['symbol']
self.description = hgnc['response']['docs'][0]['name']
# Get synonyms if requested.
if self.get_synonyms:
for item in hgnc['response']['docs'][0]['alias_symbol']:
self.synonyms.append(item)
elif hgnc['response']['numFound'] == 0:
self.error = "No results found when querying HGNC for {}".format(
self.external_id)
return self
def add_sequence_to_nodes(n: str, d: Dict[str, Any]):
"""
Maps UniProt ACC to UniProt ID. Retrieves sequence from UniProt and adds it to the node as a feature
:param n: Graph node.
:type n: str
:param d: Graph attribute dictionary.
:type d: Dict[str, Any]
"""
h = HGNC(verbose=False)
u = UniProt(verbose=False)
d["uniprot_ids"] = h.fetch(
"symbol", d["protein_id"])["response"]["docs"][0]["uniprot_ids"]
# Todo these API calls should probably be batched
# Todo mapping with bioservices to support other protein IDs?
for id in d["uniprot_ids"]:
d[f"sequence_{id}"] = u.get_fasta_sequence(id)
