def download(self, genes, fields, scope=None, species=None):
'''
Retrives the data depending on self.constraints and self.view
'''
constraints = self.constraints
views = self.views
glist = np.array(genes)
if len(glist) > 1000:
a = len(glist) / 1000
segs = np.array_split(glist, a)
else:
segs = [glist]
# store the data in here
z = []
# API uses letters to distinguish between constraints
alpha = list(string.ascii_uppercase)
for seg in segs:
# Connect to the API
service = SS(self.datasource)
query = service.new_query("Gene")
query.add_view(",".join(views))
# Some databases require a host name
if self.hostid != "":
query.add_constraint("Gene",
"LOOKUP",
",".join(seg),
self.hostid,
code="A")
else:
query.add_constraint("Gene", "LOOKUP", ",".join(seg), code="A")
# Apply the constraints
if len(constraints) != 0:
i = 1
for constraint in constraints:
letter = alpha[i]
if len(constraint.split("=")) == 2:
L = constraint.split("=")
query.add_constraint(L[0], "=", L[1], code=letter)
elif re.search("IS NOT NULL", constraint):
p1 = constraint.replace(" IS NOT NULL", "")
query.add_constraint(p1, "IS NOT NULL", code=letter)
i = i + 1
# Parse the output into a list of tuples
j = 0
for row in query.rows():
t = [row['symbol']]
for v in views:
t.append(row[v])
z.append(tuple(t))
j += 1
self.dataset = z
def test(self):
'''
Tests the HumanMine API
Look up symbol for APOBEC3G, should return APOBEC3G.
'''
service = SS('http://www.humanmine.org/humanmine/service')
query = service.new_query("Gene")
query.add_view("symbol")
query.add_constraint("Gene", "LOOKUP", "APOBEC3G", code="A")
for row in query.rows():
symbol = row['symbol']
if symbol == "APOBEC3G":
return 1
else:
return 0