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#! /usr/bin/env python
##############################################################################
## DendroPy Phylogenetic Computing Library.
##
## Copyright 2010-2015 Jeet Sukumaran and Mark T. Holder.
## All rights reserved.
##
## See "LICENSE.rst" for terms and conditions of usage.
##
## If you use this work or any portion thereof in published work,
## please cite it as:
##
## Sukumaran, J. and M. T. Holder. 2010. DendroPy: a Python library
## for phylogenetic computing. Bioinformatics 26: 1569-1571.
##
##############################################################################
"""
Benchmarking (raw) NEXUS tokenizer performance.
"""
import sys
import os
import timeit
import argparse
from dendropy.utility import messaging
from dendropy.test.support import pathmap
from dendropy.dataio import nexusprocessing
TREE_FILENAMES = [
"APG_Angiosperms.nexus",
"APG_Angiosperms.newick",
"GEBA.tree.nexus",
"GEBA.tree.newick",
"feb032009.trees.nexus",
"feb032009.trees.newick",
"Bininda-emonds_2007_mammals.nexus",
"Bininda-emonds_2007_mammals.newick",
"Jetz_et_al_2012_Aves.sample.tree.nexus",
"Jetz_et_al_2012_Aves.sample.tree.newick",
"Smith_2001_angiosperms.nexus",
"Smith_2001_angiosperms.newick",
]
CHAR_FILENAMES = [
"actinopterygii.chars.nexus",
"angiosperms.chars.nexus",
]
def tokenizing_fn_factory(src_paths, verbose=False):
def f():
for src_path in src_paths:
if verbose:
sys.stderr.write(" .. {}\n".format(src_path))
src = open(src_path, "rU")
nt = nexusprocessing.NexusTokenizer(src)
for token in nt:
pass
return f
def main():
parser = argparse.ArgumentParser(description=__doc__)
parser.add_argument("-f", "--target-file",
type=str,
dest="target_files",
default=[],
action="append",
help="Path to file to be tokenized; option may be specified multiple times for multiple files.")
parser.add_argument("-t", "--target-type",
type=str,
dest="target_types",
default=[],
choices=["trees", "chars", "all"],
action="append",
help="Input data file types (default='all' if '-f'/'--file' argument not given); option may be specified multiple times.")
parser.add_argument("-r", "--repeat",
type=int,
default=10,
help="Repeat each tokenization this number of times (default=%(default)s).")
parser.add_argument("--delimited-output",
action="store_true",
default=False,
help="Output in tab-delimited instead of aligned format")
args = parser.parse_args()
messenger = messaging.ConsoleMessenger(name="-benchmark")
src_descs = []
src_paths = []
results = []
if args.target_files:
for f in args.target_files:
ff = os.path.expanduser(os.path.expandvars(f))
src_paths.append(ff)
src_descs.append( ("User", f) )
if not args.target_types and not args.target_files:
messenger.info("No sources specified: adding default benchmark target set")
args.target_types = ["all"]
if "all" in args.target_types or "trees" in args.target_types:
for f in TREE_FILENAMES:
ff = pathmap.tree_source_path(f)
src_paths.append(ff)
src_descs.append( ("Trees", f) )
if "all" in args.target_types or "chars" in args.target_types:
for f in CHAR_FILENAMES:
ff = pathmap.char_source_path(f)
src_paths.append(ff)
src_descs.append( ("Alignment", f) )
for src_path, src_desc in zip(src_paths, src_descs):
messenger.info("Processing: '{}'".format(src_desc[1]))
t = timeit.Timer(tokenizing_fn_factory([src_path]))
result = min(t.repeat(args.repeat, 1))
messenger.info("Best time (of {} repetions): {:.10f} seconds".format(args.repeat, result))
results.append(result)
messenger.info("Benchmarking complete: all files processed")
if args.delimited_output:
result_template = "{}\t{}\t{:.10f}\n"
header_template = "{}\t{}\t{}\n"
else:
max_len1 = max(len(r[0]) for r in src_descs)
max_len2 = max(len(r[1]) for r in src_descs)
col1 = "{{:{}}}".format(max_len1)
col2 = "{{:{}}}".format(max_len2)
result_template = "[" + col1 + "] " + col2 + " {:.10f}\n"
header_template = col1 + " " + col2 + " {}\n"
sys.stdout.write(header_template.format("Type", "File", "Seconds"))
for result, src_desc in zip(results, src_descs):
sys.stdout.write(result_template.format(src_desc[0], src_desc[1], result))
if __name__ == "__main__":
main()
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