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#!/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."""
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))
)
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