indexes = N.arange(desired_length) * len(sequence) / desired_length
return [sequence[i] for i in indexes]
#
# Initialise the logging
#
logging.basicConfig(level=logging.INFO)
#
# Parse options
#
option_parser = OptionParser()
TestHarness.add_options(option_parser)
option_parser.add_option(
'--num-roc-points',
dest='num_points',
type='int',
default=24,
help="Number of points on each ROC curve."
)
option_parser.add_option(
'--num-negative',
dest='num_negative',
type='int',
default=50,
help="Number of negative examples used for AUC50 calculation."
)
options, args = option_parser.parse_args()
from optparse import OptionParser
from test_harness_2 import TestHarness
#
# Initialise the logging
#
format = '%(asctime)-15s %(message)s'
logging.basicConfig(level=logging.INFO, format=format)
logging.info('Command line: %s', ' '.join(sys.argv))
logging.info('Current working directory: %s', os.getcwd())
#
# Parse the options
#
option_parser = OptionParser()
TestHarness.add_options(option_parser)
option_parser.add_option("--roc-dir",
dest="roc_dir",
default='.',
help="Directory ROC files are stored in.")
options, args = option_parser.parse_args()
for option in option_parser.option_list:
if option.dest:
logging.info('%30s: %30s (%s)', option.dest,
str(getattr(options, option.dest)), option.help)
dirs = map(test_harness_methods.load_dir, args)
keys = set()
for dir in dirs:
keys.update(dir.files.keys())
fragments = set(f for f, i in keys)
# Initialise the logging
#
format = "%(asctime)-15s %(message)s"
logging.basicConfig(level=logging.INFO, format=format)
file_handler = logging.FileHandler("launch_pssm_score.log")
file_handler.setFormatter(logging.Formatter(format))
logging.getLogger("").addHandler(file_handler)
logging.info("Command line: %s", " ".join(sys.argv))
logging.info("Current working directory: %s", os.getcwd())
#
# Parse the options
#
option_parser = OptionParser()
TestHarness.add_options(option_parser)
option_parser.add_option(
"-j", "--num-threads", dest="num_threads", type="int", default=5, help="How many threads to run."
)
option_parser.add_option("--pssm-dir", dest="pssm_dir", default=".", help="Directory PSSM files are stored in.")
option_parser.add_option(
"--glam2-format",
dest="glam2_format",
default=False,
action="store_true",
help="Algorithm output files are in GLAM2 format.",
)
options, args = option_parser.parse_args()
for option in option_parser.option_list:
if option.dest:
logging.info("%30s: %30s (%s)", option.dest, str(getattr(options, option.dest)), option.help)
from test_harness_2 import TestHarness
#
# Initialise the logging
#
format = "%(asctime)-15s %(message)s"
logging.basicConfig(level=logging.INFO, format=format)
logging.info("Command line: %s", " ".join(sys.argv))
logging.info("Current working directory: %s", os.getcwd())
#
# Parse the options
#
option_parser = OptionParser()
TestHarness.add_options(option_parser)
option_parser.add_option("--roc-dir", dest="roc_dir", default=".", help="Directory ROC files are stored in.")
options, args = option_parser.parse_args()
for option in option_parser.option_list:
if option.dest:
logging.info("%30s: %30s (%s)", option.dest, str(getattr(options, option.dest)), option.help)
dirs = map(test_harness_methods.load_dir, args)
keys = set()
for dir in dirs:
keys.update(dir.files.keys())
fragments = set(f for f, i in keys)
tex = open("methods.tex", "w")
for fragment in fragments:
print >> tex, """
%s\\\\
if len(sequence) < desired_length:
raise RuntimeError('Cannot reduce sequence to longer length.')
indexes = N.arange(desired_length) * len(sequence) / desired_length
return [sequence[i] for i in indexes]
#
# Initialise the logging
#
logging.basicConfig(level=logging.INFO)
#
# Parse options
#
option_parser = OptionParser()
TestHarness.add_options(option_parser)
option_parser.add_option('--num-roc-points',
dest='num_points',
type='int',
default=24,
help="Number of points on each ROC curve.")
option_parser.add_option(
'--num-negative',
dest='num_negative',
type='int',
default=50,
help="Number of negative examples used for AUC50 calculation.")
options, args = option_parser.parse_args()
for option in option_parser.option_list:
if option.dest:
logging.info('%30s: %30s (%s)', option.dest,
import logging, sys
from test_harness_2 import TestHarness, build_hmm_model
from glam2 import GLAM2Output
from parse_gapped_format import parse_models, build_hmm_from_semi_parsed
from optparse import OptionParser
#
# Initialise the logging
#
logging.basicConfig(level=logging.INFO)
#
# Parse options
#
option_parser = OptionParser()
TestHarness.add_options(option_parser)
option_parser.add_option("-q",
dest="quiet",
action='store_true',
default=False,
help="Run quietly.")
option_parser.add_option("--glam2-format",
dest="glam2_format",
default=False,
action="store_true",
help="Algorithm output files are in GLAM2 format.")
options, args = option_parser.parse_args()
if options.quiet:
logging.getLogger().setLevel(logging.WARNING)
for option in option_parser.option_list:
if option.dest:
# Initialise the logging
#
format='%(asctime)-15s %(message)s'
logging.basicConfig(level=logging.INFO, format=format)
file_handler = logging.FileHandler('launch_pssm_score.log')
file_handler.setFormatter(logging.Formatter(format))
logging.getLogger('').addHandler(file_handler)
logging.info('Command line: %s', ' '.join(sys.argv))
logging.info('Current working directory: %s', os.getcwd())
#
# Parse the options
#
option_parser = OptionParser()
TestHarness.add_options(option_parser)
option_parser.add_option(
"-j",
"--num-threads",
dest="num_threads",
type='int',
default=5,
help="How many threads to run."
)
option_parser.add_option(
"--pssm-dir",
dest="pssm_dir",
default='.',
help="Directory PSSM files are stored in."
)
option_parser.add_option(
from glam2 import GLAM2Output from parse_gapped_format import parse_models, build_hmm_from_semi_parsed from optparse import OptionParser # # Initialise the logging # logging.basicConfig(level=logging.INFO) # # Parse options # option_parser = OptionParser() TestHarness.add_options(option_parser) option_parser.add_option( "-q", dest="quiet", action='store_true', default=False, help="Run quietly." ) option_parser.add_option( "--glam2-format", dest="glam2_format", default=False, action="store_true", help="Algorithm output files are in GLAM2 format." ) options, args = option_parser.parse_args()
