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#!/usr/bin/env python
# encoding: utf-8
"""
untitled.py
Created by Cole Trapnell on 2007-05-01.
Copyright (c) 2007 __MyCompanyName__. All rights reserved.
"""
import sys
import getopt
import os
import time
import timeit
import csv
help_message = '''
This script runs the full cmatch experimental suite.
'''
class Usage(Exception):
def __init__(self, msg):
self.msg = msg
#refs = ["NC_005810", "2","NC_003997"]
#qry_lengths = [25, 50, 200, 800]
refs = ["NC_003997"]
qry_lengths = [25]
def get_stats(filename):
stats = {}
statfile = open(filename)
stats = dict([(key, float(value)) for (key, value) in csv.reader(statfile)])
return stats
def cmatch_query_string(ref, length):
return ref + "_q" + str(length) + "bp.fna"
def mummer_query_string(ref, length):
return ref + "_q" + str(length) + "bp.fna"
def runCmatch(ref, query, matchlen, onCPU, outfile):
if onCPU:
cpuFlag = "-C"
statfile = "%s-%ld.cpustats" % ( query, matchlen )
else:
cpuFlag = ""
statfile = "%s-%ld.gpustats" % ( query, matchlen )
match_flags = " -l %d " % (matchlen)
cmd = "mummergpu %s -s %s -M -b %s %s %s > %s" % (cpuFlag,
statfile,
match_flags,
ref,
query,
outfile)
print >> sys.stderr, cmd
t = timeit.Timer("os.system('" + cmd + "')", "import os")
app_times = t.repeat(1, 1)
app_time_avg = sum(app_times)/len(app_times)
stats = get_stats(statfile)
return (app_time_avg, stats)
def runMUMmer(ref, query, matchlen, outfile):
query_file = query
#for i in range(0,5):
# query_files += query + " "
cmd = "mummer -maxmatch -b -l %d %s %s 2>/dev/null > %s" % (matchlen,
ref,
query_file,
outfile)
print >> sys.stderr , cmd
t = timeit.Timer("os.system('" + cmd + "')", "import os")
app_times = t.repeat(1, 1)
app_time_avg = sum(app_times)/len(app_times)
return app_time_avg
def get_gpu_time(stats):
return stats["Kernel"] + stats["Copy queries to GPU"] + stats["Copy output from GPU"] + stats["Copy suffix tree to GPU"]
def execute_synth_trial(fout, directory, ref, querylen, matchlen):
#cmatch_query_file = directory + "/" + ref + query
query_file = "%s/%s_q%dbp.fna" % (directory, ref, querylen)
ref_file = "%s/%s.fna" % (directory, ref)
cpu_outfile = query_file + "-cpu.out"
gpu_outfile = query_file + "-gpu.out"
mummer_outfile = query_file + "-mummer.out"
(gpu_app_time_avg, gpu_stats) = runCmatch(ref_file,
query_file,
matchlen,
False,
gpu_outfile)
(cpu_app_time_avg, cpu_stats) = runCmatch(ref_file,
query_file,
matchlen,
True,
cpu_outfile)
mummer_app_time_avg = runMUMmer(ref_file, query_file, matchlen == 0 and querylen or matchlen, mummer_outfile)
kernel_speedup = cpu_stats["Kernel"] / get_gpu_time(gpu_stats)
print >>fout, querylen, matchlen, cpu_app_time_avg,gpu_app_time_avg, mummer_app_time_avg, cpu_app_time_avg / gpu_app_time_avg, mummer_app_time_avg / gpu_app_time_avg, kernel_speedup
#print cmd
def execute_real_trial(fout, directory, ref, query, matchlen):
ref_file = "%s/%s.fna" % (directory, ref)
query_file = "%s/%s.fna" % (directory, query)
cpu_outfile = query_file + "-cpu.out"
gpu_outfile = query_file + "-gpu.out"
mummer_outfile = query_file + "-mummer.out"
(gpu_app_time_avg, gpu_stats) = runCmatch(ref_file,
query_file,
matchlen,
False,
gpu_outfile)
(cpu_app_time_avg, cpu_stats) = runCmatch(ref_file,
query_file,
matchlen,
True,
cpu_outfile)
mummer_app_time_avg = runMUMmer(ref_file, query_file, matchlen, mummer_outfile)
kernel_speedup = cpu_stats["Kernel"] / get_gpu_time(gpu_stats)
print >> fout, "-", matchlen,cpu_app_time_avg,gpu_app_time_avg, mummer_app_time_avg, cpu_app_time_avg / gpu_app_time_avg, mummer_app_time_avg / gpu_app_time_avg, kernel_speedup
def run_different_query_lengths():
f = open("anthrax/speedup.out", "w")
print >> f, "QUERY,MATCH_LENGTH,CPU,GPU,MUMMER,CPU_SPEEDUP,MUMMER_SPEEDUP,KERNEL_SPEEDUP"
execute_synth_trial(f,"anthrax", "NC_003997", 25, 25)
execute_synth_trial(f,"anthrax", "NC_003997", 50, 50)
execute_synth_trial(f,"anthrax", "NC_003997", 100,100)
execute_synth_trial(f,"anthrax", "NC_003997", 200,200)
execute_synth_trial(f,"anthrax", "NC_003997", 400,400)
execute_synth_trial(f,"anthrax", "NC_003997", 800,800)
def run_ssuis_solexa():
f = open("s_suis/speedup.out", "w")
print >> f, "QUERY,MATCH_LENGTH,CPU,GPU,MUMMER,CPU_SPEEDUP,MUMMER_SPEEDUP,KERNEL_SPEEDUP"
execute_real_trial(f,"s_suis", "cleanref", "cleanreads", 20)
def run_cereus_454():
f = open("cereus/speedup.out", "w")
print >> f, "QUERY,MATCH_LENGTH,CPU,GPU,MUMMER,CPU_SPEEDUP,MUMMER_SPEEDUP,KERNEL_SPEEDUP"
execute_real_trial(f,"cereus", "cleanref", "cleanreads", 20)
def run_briggsae_sanger():
f = open("cbriggsae/speedup.out", "w")
print >> f, "QUERY,MATCH_LENGTH,CPU,GPU,MUMMER,CPU_SPEEDUP,MUMMER_SPEEDUP,KERNEL_SPEEDUP"
execute_real_trial(f,"cbriggsae", "cleanref", "cleanreads", 100)
def main(argv=None):
if argv is None:
argv = sys.argv
try:
try:
opts, args = getopt.getopt(argv[1:], "hv", ["help"])
except getopt.error, msg:
raise Usage(msg)
for option, value in opts:
if option == "-v":
verbose = True
if option in ("-h", "--help"):
raise Usage(help_message)
run_ssuis_solexa()
run_cereus_454()
run_briggsae_sanger()
run_different_query_lengths()
except Usage, err:
print >> sys.stderr, sys.argv[0].split("/")[-1] + ": " + str(err.msg)
print >> sys.stderr, "\t for help use --help"
return 2
if __name__ == "__main__":
sys.exit(main())
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