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#!/usr/bin/env python3
# Needs the /usr/bin/time program: apt install time
# Example: ./benchmark.py ~/Devel/bali-phy/git 10 --dir ~/Work --old ~/Devel/bali-phy/old/bali-phy-3.6.0/bin/bali-phy
# See https://llvm.org/docs/Benchmarking.html
import argparse
import re
import subprocess
import sys
import tempfile
import statistics
import os
from git import Repo
import shutil
import logging
from pathlib import Path
def get_times(cmd, cwd, shield=True):
tmpfile = tempfile.NamedTemporaryFile()
cmd = ['time' ,'-p','-o', tmpfile.name] + cmd
if shield:
cmd = ["cset", "shield", "--exe", "--"] + cmd
result = subprocess.run(cmd, capture_output=True, cwd=cwd)
if result.returncode != 0:
print(result.stderr.decode(),file=sys.stderr)
return None
times = dict()
tmpfile.seek(0)
for line in tmpfile:
m = re.match('([^ ]*) +([^ ]*)', line.decode())
if m:
times[m.group(1)] = float(m.group(2))
return times
def benchmark(n, name, cmd, cwd):
times = []
for i in range(n):
print(f"testing {name}: iter {i+1}/{n} ",end='', flush=True)
time = get_times(cmd+[f'--seed={i}'], cwd)["real"];
print(f' {time}s')
times.append(time)
return times
def exec_show_result(cmd, **kwargs):
showcmd = ' '.join([f"'{word}'" for word in cmd])
subargs = dict()
if "infile" in kwargs:
infile = kwargs["infile"]
subargs["stdin"] = open(infile,encoding='utf-8')
showcmd += f" < '{infile}'"
elif "stdin" in kwargs:
subargs["stdin"] = kwargs["stdin"]
if "outfile" in kwargs:
outfile = kwargs["outfile"]
subargs["stdout"] = open(outfile,'w+',encoding='utf-8')
showcmd += f" > '{outfile}'"
elif "stdout" in kwargs:
subargs["stdout"] = kwargs["stdout"]
else:
subargs["stdout"] = subprocess.PIPE
if "errfile" in kwargs:
errfile = kwargs["errfile"]
subargs["stderr"] = open(errfile,'w+',encoding='utf-8')
showcmd += f" 2> '{errfile}'"
elif "stderr" in kwargs:
subargs["stderr"] = kwargs["stderr"]
else:
subargs["stderr"] = subprocess.PIPE
if "cwd" in kwargs:
subargs["cwd"] = kwargs["cwd"]
logging.debug(showcmd)
result = subprocess.run(cmd,**subargs)
if result.returncode != 0:
print(f"command: {showcmd}",file=sys.stderr)
if "outfile" in kwargs and path.exists(kwargs["outfile"]):
os.remove(kwargs["outfile"])
if "errfile" in kwargs and path.exists(kwargs["errfile"]):
os.remove(kwargs["errfile"])
if "handler" in kwargs:
handler = kwargs["handler"]
handler(result.returncode)
elif "verbose" in kwargs and kwargs["verbose"]:
print(f"\n\t{showcmd}\n")
return result
def exec_show(cmd, **kwargs):
result = exec_show_result(cmd, **kwargs)
out_message = None
if "stdout" not in kwargs and "outfile" not in kwargs:
out_message = result.stdout.decode('utf-8')
err_message = None
if "stderr" not in kwargs and "errfile" not in kwargs:
err_message = result.stderr.decode('utf-8')
# Always record error messages in the log file.
if err_message:
logging.info(f" err: {err_message}")
if out_message:
logging.debug(f" out: {out_message}")
code = result.returncode
if code != 0:
logging.info(f" exit: {code}")
logging.info(f" exit: {code}")
if out_message:
logging.info(f" out: {out_message}")
print(f" out: {out_message}", file=sys.stdout)
if err_message:
logging.info(f" err: {err_message}")
if "stop_on_error" in kwargs and kwargs["stop_in_error"]:
exit(code)
return (out_message, result)
def configure(source_dir, build_dir, install_parent):
if not os.path.isdir(build_dir):
os.mkdir(build_dir)
meson_out, meson_result = exec_show(['meson','setup', source_dir, build_dir, f'--prefix={install_parent}', '--reconfigure'])
if meson_result.returncode != 0:
sys.stderr.write(f"Removing directory {build_dir}!\n")
logging.warning(f"Removing directory {build_dir}!")
shutil.rmtree(build_dir)
return False
else:
return True
else:
meson_out, meson_result = exec_show(['meson','setup', source_dir, build_dir, f'--prefix={install_parent}', '--reconfigure'])
if meson_result.returncode != 0:
return False
else:
return True;
def do_compile(build_dir):
meson_out, meson_result = exec_show(['meson','install', '-C', build_dir])
return meson_result.returncode == 0
def build(source_dir, build_dir, install_parent):
if configure(source_dir, build_dir, install_parent):
logging.info("configure: OK")
if do_compile(build_dir):
logging.info("compile: OK")
return os.path.join(install_parent, "bin", "bali-phy")
else:
logging.info("compile: failed")
else:
logging.info("configure: failed")
return None
parser = argparse.ArgumentParser(description="Extract the consensus sequence for a chromosome from a bam file",
epilog= "Example: benchmark.py ERR2679006_dedup_reads.bam PVP01.fasta ERR2679006 --chromosome LT635626 --min-coverage 1 3 5 10 20")
parser.add_argument("repo", help="Path to repo")
parser.add_argument("count", help="Number of commits to benchmark")
parser.add_argument("--dir", default=".", help="Directory to run in")
parser.add_argument("--build", default="build",help="Directory to build in")
parser.add_argument("--install",default="local",help="Directory to install in")
parser.add_argument("--verbose",help="Be verbose",action='store_true')
parser.add_argument("--reps", type=int, default=10, help="Be verbose")
#parser.add_argument("reference", help="Reference file used to map the bam file (.fasta)")
#parser.add_argument("--chromosome", help="The chromosome from which to extract the consensus sequence")
#parser.add_argument("--min-quality", default=25, type=int, help="Quality score required for a base in a read to count (default is 25)")
#parser.add_argument("--min-coverage", default=[2], type=int,nargs='+',help="Number of high quality score reads required to make a call (default is 2)")
#parser.add_argument("--max-coverage",type=int, help="Ignore reference locations with coverage higher than this")
#parser.add_argument("--prefix", help="Prefix chromosome names with this")
#parser.add_argument("--min-mapping-quality", default=1, type=int,nargs='+',help="Skip reads with a lower mapping quality (default is 1)")
#parser.add_argument("--max-soft-clipped", type=int, default=0, help="Skip reads with a higher number of soft-clipped bases (default is 0)")
#parser.add_argument("output", help="Output prefix")
args = parser.parse_args()
if args.verbose:
logging.basicConfig(level=0)
else:
logging.basicConfig(level=15)
build_dir = Path(args.build).resolve()
install_dir = Path(args.install).resolve()
run_dir = Path(args.dir)
#1. Find the repo and get the list of commits to analyze
repo = Repo(args.repo)
commits = list(repo.iter_commits(max_count=args.count))
for commit in commits:
# checkout the commit by running `git checkout {commit}`
logging.info(f"Checking out commit {commit}")
repo.git.checkout(commit)
logging.info(f"Building executable {commit}")
exe = build(args.repo, build_dir, install_dir)
cmd = [exe, '48-muscle.fasta', '--pre-burnin=0', '--iter=25']
#cmd = ['ls','/dev/']
#cmd = ['ls','/usr/share/doc/']
print(f"cmd = {cmd}", file=sys.stderr)
times = benchmark(args.reps, "sha", cmd, run_dir)
med_time = statistics.median(times)
sigma_time = statistics.stdev(times)
print(f"time = {med_time:.2f} +- {sigma_time:.2f} {commit.message}")
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