def kmer_to_repbase_with_mongo(kmer_file):
client = MongoClient()
client = MongoClient('mongodb://localhost:27017/')
db = client.Repbase
index = db.MainIndex
name_index = db.NameIndex
name_hash = {}
print "Iter over kmers"
for d in sc_iter_simple_tab_file(kmer_file):
(kmer, tf) = d
kmer = kmer.lower()
print kmer, tf
data = index.find_one({'kmer':kmer})
if not data:
rkmer = get_revcomp(kmer)
data = index.find_one({'kmer':rkmer})
if data:
matches = data["index"]
for rid, tf in matches:
if rid in name_hash:
name = name_hash[rid]
else:
name = name_index.find_one({"kid":rid})
name = name["name"]
name_hash[rid] = name
print "\t", name, tf
else:
print "\t???"
def kmer_to_cegma_with_mongo(kmer_file, verbose=False):
client = MongoClient()
client = MongoClient('mongodb://localhost:27017/')
db = client.Repbase
index = db.CegmaMainIndex
name_index = db.CegmaNameIndex
repbase_index = db.MainIndex
name_hash = {}
print "Iter over kmers"
match = {
"repbase": 0,
"cegma": 0,
"repbase_cegma": 0,
"other": 0,
}
match_distr = {
"repbase": defaultdict(int),
"cegma": defaultdict(int),
"repbase_cegma": defaultdict(int),
"other": defaultdict(int),
}
for d in sc_iter_simple_tab_file(kmer_file):
(kmer, tf) = d
repbase_hit = False
cegma_hit = False
# print tf, kmer, "\r",
tf = int(tf)
print match, tf, "\r",
kmer = kmer.lower()
# if verbose:
# print tf, kmer, "\r",
data = repbase_index.find_one({'kmer':kmer})
if not data:
rkmer = get_revcomp(kmer)
data = repbase_index.find_one({'kmer':rkmer})
if data:
repbase_hit = True
data = index.find_one({'kmer':kmer})
if not data:
rkmer = get_revcomp(kmer)
data = index.find_one({'kmer':rkmer})
if data:
matches = data["index"]
cegma_hit = True
# print
# print kmer, tf
# for rid, tf in matches:
# if rid in name_hash:
# name = name_hash[rid]
# else:
# name = name_index.find_one({"kid":rid})
# name = name["name"].strip()
# name_hash[rid] = name
# print "\t", name, tf
# else:
# # print "\t???"
# pass
if repbase_hit and cegma_hit:
match["repbase_cegma"] += 1
match_distr["repbase_cegma"][tf] += 1
continue
elif repbase_hit:
match["repbase"] += 1
match_distr["repbase"][tf] += 1
continue
elif cegma_hit:
match["cegma"] += 1
match_distr["cegma"][tf] += 1
continue
else:
match["other"] += 1
print
print match_distr
print match
