def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-t",
"--test",
dest="test",
type="string",
help="supply help")
parser.add_option("--time",
dest="timepoints",
type="string",
help="a comma-separated list of time points measured")
parser.add_option("--replicates",
dest="reps",
type="string",
help="a comma-separated list of replicate IDs")
parser.add_option("--condition",
dest="condition",
type="string",
help="experimental condition")
parser.add_option("--resamples",
dest="resamples",
type="string",
help="number of times to resample replicates to"
" generate pseudo datasets")
parser.add_option("--input-gtf",
dest="gtf_file",
type="string",
help="reference gtf file")
parser.add_option("--output-file-directory",
dest="output_dir",
type="string",
help="directory to output"
" resampled files to")
# add common options (-h/--help, ...) and parse command line
(options, args) = E.start(parser, argv=argv)
try:
infile = IOTools.open_file(argv[-1], "r")
except IOError:
infile = options.stdin
data_frame = pd.read_table(infile, sep="\t", index_col=0, header=0)
time_str = options.timepoints.split(",")
time_points = [int(x) for x in time_str]
replicates = options.reps.split(",")
reps = int(options.resamples)
its = [time_str, replicates]
midx = pd.MultiIndex.from_product(its, names=['times', 'replicates'])
TS.genResampleData(data_frame=data_frame,
multiple_index=midx,
replicates=reps,
sample_reps=replicates,
times=time_points,
condition=options.condition,
ref_gtf=options.gtf_file,
out_dir=options.output_dir,
seed=int(options.random_seed))
# Write footer and output benchmark information.
E.stop()
def main(argv=None):
"""script main.
parses command line options in sys.argv, unless *argv* is given.
"""
if argv is None:
argv = sys.argv
# setup command line parser
parser = E.OptionParser(version="%prog version: $Id$",
usage=globals()["__doc__"])
parser.add_option("-t", "--test", dest="test", type="string",
help="supply help")
parser.add_option("--time", dest="timepoints", type="string",
help="a comma-separated list of time points measured")
parser.add_option("--replicates", dest="reps", type="string",
help="a comma-separated list of replicate IDs")
parser.add_option("--condition", dest="condition", type="string",
help="experimental condition")
parser.add_option("--resamples", dest="resamples", type="string",
help="number of times to resample replicates to"
" generate pseudo datasets")
parser.add_option("--input-gtf", dest="gtf_file", type="string",
help="reference gtf file")
parser.add_option("--output-file-directory", dest="output_dir",
type="string", help="directory to output"
" resampled files to")
# add common options (-h/--help, ...) and parse command line
(options, args) = E.Start(parser, argv=argv)
try:
infile = IOTools.openFile(argv[-1], "r")
except IOError:
infile = options.stdin
data_frame = pd.read_table(infile,
sep="\t",
index_col=0,
header=0)
time_str = options.timepoints.split(",")
time_points = [int(x) for x in time_str]
replicates = options.reps.split(",")
reps = int(options.resamples)
its = [time_str, replicates]
midx = pd.MultiIndex.from_product(its,
names=['times', 'replicates'])
TS.genResampleData(data_frame=data_frame,
multiple_index=midx,
replicates=reps,
sample_reps=replicates,
times=time_points,
condition=options.condition,
ref_gtf=options.gtf_file,
out_dir=options.output_dir,
seed=int(options.random_seed))
# Write footer and output benchmark information.
E.Stop()
