def get(self, term):
hgene_results = list(homologene.filter(
(homologene.gene_symbol == term) or
(homologene.protein_gi == term) or
(homologene.protein_accession == term))
.select(homologene.gene_symbol,
homologene.ce_gene_name,
homologene.species)
.distinct()
.dicts().execute())
wbgene_results = list(wb_orthologs.filter(
(wb_orthologs.gene_symbol == term) or
(wb_orthologs.ortholog == term))
.select(wb_orthologs.gene_symbol,
wb_orthologs.ce_gene_name,
wb_orthologs.species)
.distinct()
.dicts().execute())
for x in hgene_results:
x.update({"source": "homologene"})
for x in wbgene_results:
x.update({"source": "wormbase"})
homologs = hgene_results + wbgene_results
# For genes that can't be looked up, fetch coordinates.
for x in homologs:
if x["ce_gene_name"].find(".") > 0:
try:
gene = wb_gene.get(
wb_gene.sequence_name == x["ce_gene_name"])
x.update(
{"CHROM": gene.CHROM,
"start": gene.start,
"end": gene.end})
except:
del x
result = hgene_results + wbgene_results
return jsonify(result)
def omim(gene_name):
gene_id = wb_gene.get(Name = gene_name)
r = requests.get('http://www.wormbase.org/rest/widget/gene/%s/human_diseases' % gene_id.Name,
headers = {'Content-Type': 'application/json; charset=utf-8'}).json()
r = r["fields"]["human_diseases"]["data"]
omim_models, omim_genes, omim_diseases, response = {}, [], [], {}
if r:
if "potential_model" in r:
omim_models = {x["id"]:x["label"] for x in r["potential_model"]}
if "gene" in r:
omim_genes = r["gene"]
if "disease" in r:
omim_diseases = r["disease"]
api_key = ds.get(ds.key("credential", "OMIM"))["apiKey"]
omim_url = "http://api.omim.org/api/entry?mimNumber={omim_ids}&apiKey={api_key}"
omim_url = omim_url.format(omim_ids = ','.join(omim_genes + omim_diseases), api_key = api_key)
omim_results = requests.get(omim_url).text
dom = minidom.parseString(omim_results)
omim_results = {x[1].firstChild.nodeValue:
x[0].firstChild.nodeValue for x in zip(dom.getElementsByTagName("preferredTitle"),
dom.getElementsByTagName("mimNumber"))}
response = {"omim_diseases": {x: omim_results[x] for x in omim_diseases},
"omim_genes" : {x: omim_results[x] for x in omim_genes}}
return jsonify(response)