def blast(Gene_id, Blast_data):
ID = []
i = 0
file1 = open(Gene_id, "r")
file2 = open(Blast_data, "w")
for k in file1:
ID.append(k)
while i != len(ID):
for id in TogoWS.search_iter("gene", ID[i], limit=1):
file2.write(id)
i += 1
def check(self, database, search_term, expected_matches=(), limit=None):
if expected_matches and limit:
raise ValueError("Bad test - TogoWS makes no promises about order")
search_count = TogoWS.search_count(database, search_term)
if expected_matches and search_count < len(expected_matches):
raise ValueError("Only %i matches, expected at least %i" % (search_count, len(expected_matches)))
if search_count > 5000 and not limit:
print("%i results, skipping" % search_count)
return
if limit:
count = min(search_count, limit)
else:
count = search_count
# Iteration should find everything... unless a limit is used
search_iter = list(TogoWS.search_iter(database, search_term, limit))
self.assertEqual(count, len(search_iter))
for match in expected_matches:
self.assertTrue(match in search_iter, "Expected %s in results but not" % match)
def check(self, database, search_term, expected_matches=[], limit=None):
if expected_matches and limit:
raise ValueError("Bad test - TogoWS makes no promises about order")
search_count = TogoWS.search_count(database, search_term)
if expected_matches and search_count < len(expected_matches):
raise ValueError("Only %i matches, expected at least %i" \
% (search_count, len(expected_matches)))
if search_count > 5000 and not limit:
print "%i results, skipping" % search_count
return
if limit:
count = min(search_count, limit)
else:
count = search_count
#Iteration should find everything... unless a limit is used
search_iter = list(TogoWS.search_iter(database, search_term, limit))
self.assertEqual(count, len(search_iter))
for match in expected_matches:
self.assert_(match in search_iter,
"Expected %s in results but not" % match)
def check(self, database, search_term, expected_matches=(), limit=None):
if expected_matches and limit:
raise ValueError("Bad test - TogoWS makes no promises about order")
try:
search_count = TogoWS.search_count(database, search_term)
except HTTPError as err:
raise ValueError("%s from %s" % (err, err.url)) from None
if expected_matches:
self.assertGreaterEqual(search_count, len(expected_matches))
if search_count > 5000 and not limit:
print("%i results, skipping" % search_count)
return
if limit:
count = min(search_count, limit)
else:
count = search_count
# Iteration should find everything... unless a limit is used
search_iter = list(TogoWS.search_iter(database, search_term, limit))
self.assertEqual(count, len(search_iter))
for match in expected_matches:
self.assertIn(match, search_iter, "Expected %s in results" % match)
