1
2
3
4
5
6
7
8
9
10
11
12
13
14
15
16
17
18
19
20
21
22
23
24
25
26
27
28
29
30
31
32
33
34
35
36
37
38
39
40
41
42
43
44
45
46
47
48
49
50
51
52
53
54
|
#!/usr/bin/env python
# Copyright 2002 Brad Chapman. All rights reserved.
#
# This code is part of the Biopython distribution and governed by its
# license. Please see the LICENSE file that should have been included
# as part of this package.
"""Test timing of getting records from a BioSQL database."""
from __future__ import print_function
import time
# set up the connection
from BioSQL import BioSeqDatabase
server = BioSeqDatabase.open_database(host="192.168.0.192", user="root",
passwd="", db="test_biosql")
db = server["embl_rod"]
# -- do the fasta-only timing part
start_time = time.time()
num_records = 0
for junk_id, record in db.items():
num_records += 1
sequence = record.seq.data
d = record.description
i = record.id
n = record.name
end_time = time.time()
elapsed_time = end_time - start_time
print("Fasta")
print("\tDid %s records in %s seconds for\n\t%f records per second" %
(num_records, elapsed_time, float(num_records) / float(elapsed_time)))
# -- do the "EMBL" timing part
start_time = time.time()
num_records = 0
for junk_id, record in db.items():
num_records += 1
sequence = record.seq.data
d = record.description
i = record.id
n = record.name
features = record.features
anns = record.annotations
dates = record.dates
species = record.species
keywords = record.keywords
end_time = time.time()
elapsed_time = end_time - start_time
print("EMBL")
print("\tDid %s records in %s seconds for\n\t%f records per second" %
(num_records, elapsed_time, float(num_records) / float(elapsed_time)))
|
