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#!/usr/bin/env python
""" A simple client waiting for data to clean up 454 sequencing data"""
__author__ = "Jens Reeder"
__copyright__ = "Copyright 2011, The QIIME Project"
__credits__ = ["Jens Reeder", "Rob Knight"]#remember to add yourself if you make changes
__license__ = "GPL"
__version__ = "1.4.0"
__maintainer__ = "Jens Reeder"
__email__ = "jens.reeder@gmail.com"
__status__ = "Release"
from qiime.util import parse_command_line_parameters, get_options_lookup,\
make_option
from qiime.denoiser.utils import get_denoiser_data_dir
from qiime.denoiser.denoise_worker import setup_worker
options_lookup = get_options_lookup()
#denoiser_worker.py
script_info={}
script_info['brief_description'] = "Start a denoiser worker process"
script_info['script_description'] = """The workers are automatically started by the denoiser.py script.
You usually never need to use this script yourself.
A worker waits for data and does flowgram alignments once it gets it."""
script_info['script_usage'] = [ \
( "",
"Start worker and connect to server listening on port 12345 on the same machine (localhost)",
"%prog -f seqs.fna -f denoiser_out/worker99 -p 12345 -s localhost")
]
script_info['output_description']="Denoise worker writes a log file if verbose flag is set."
script_info['required_options']=[\
make_option('-f','--file_path',action='store',\
type='string',dest='file_path',\
help='path used as prefix for worker data files'+\
'[REQUIRED]'),
make_option('-p','--port', action='store',\
type='int', dest='port', help='Server port '+\
'[REQUIRED]'),
make_option('-s','--server_address',action='store',\
type='string',dest='server',help='Server address'+\
'[REQUIRED]' )
]
script_info['optional_options']=[ \
make_option('-e','--error_profile',action='store',\
type='string',dest='error_profile',\
help='Path to error profile'+\
' [DEFAULT: %default]',\
default = get_denoiser_data_dir()+\
'FLX_error_profile.dat'),
make_option('-c','--counter', action='store',\
type='int', dest='counter',\
help='Round counter to start this worker with '+\
' [default: %default]', default=0)
]
script_info['version'] = __version__
def main(commandline_args=None):
parser, opts, args = parse_command_line_parameters(**script_info)
if not opts.file_path:
parser.error("Required option --file_path not specified.")
if not opts.port:
parser.error("Required option --port not specified.")
if not opts.server:
parser.error("Required options --server_address not specified.")
setup_worker(opts.file_path, opts.server, opts.port,
opts.counter, opts.verbose, opts.error_profile)
if __name__ == "__main__":
main()
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