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Sourcecode: python-biopython version File versions

biosql_performance_read.py

#/usr/bin/env python
"""Small script to 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()
all_records = db.items()
for junk_id, record in all_records:
    sequence = record.seq.data
    d = record.description
    i = record.id
    n = record.name 

end_time = time.time()
num_records = len(all_records)
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()
all_records = db.items()
for junk_id, record in all_records:
    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()
num_records = len(all_records)
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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