def testCachedValidation(self):
try:
import dogpile.cache
except:
pass
else:
r = pathmap.get_test_repos()
p = Phylesystem(r)
nexson, sha = p.return_study('xy_10')
r = p.add_validation_annotation(nexson, sha)
cache_hits = p._cache_hits
r1 = p.add_validation_annotation(nexson, sha)
self.assertEqual(1 + cache_hits, p._cache_hits)
self.assertEqual(r, r1)
import sys; from peyotl import write_as_json;
write_as_json(nexson, sys.stdout)
def testCachedValidation(self):
try:
# noinspection PyPackageRequirements
import dogpile.cache
except:
pass
else:
r = pathmap.get_test_repos()
p = Phylesystem(r)
nexson, sha = p.return_study('xy_10')
r = p.add_validation_annotation(nexson, sha)
cache_hits = p._cache_hits
r1 = p.add_validation_annotation(nexson, sha)
self.assertEqual(1 + cache_hits, p._cache_hits)
self.assertEqual(r, r1)
write_as_json(nexson, sys.stdout)
def testCachedValidation(self):
try:
import dogpile.cache
except:
pass
else:
r = pathmap.get_test_repos()
p = Phylesystem(r)
nexson, sha = p.return_study('xy_10')
r = p.add_validation_annotation(nexson, sha)
cache_hits = p._cache_hits
r1 = p.add_validation_annotation(nexson, sha)
self.assertEqual(1 + cache_hits, p._cache_hits)
self.assertEqual(r, r1)
import sys
from peyotl import write_as_json
write_as_json(nexson, sys.stdout)
print study_id
'''
study_id = sys.argv[1]
tree_id = sys.argv[2]
seqaln = sys.argv[3]
mattype = sys.argv[4]
runname = sys.argv[5]
#Fixed values
E_VALUE_THRESH = 0.04
ott_ncbi = "../ott_ncbi" #TODO config file
Entrez.email = "*****@*****.**"
phy = Phylesystem()
n = phy.return_study(study_id)[0]
api_wrapper.study.get(study_id, tree=tree_id)
##This is a weird way to get the ingroup node, but I need the OTT ids anyhow.
m = extract_tree(n,
tree_id,
PhyloSchema('newick',
output_nexml2json='1.2.1',
content="tree",
tip_label="ot:ottId"),
subtree_id="ingroup")
otu_dict = gen_otu_dict(n)
ottids = []
for oid, o in otu_dict.items():
try:
ottid = o[u'^ot:ottId']
