def test_get_denoiser_data_dir(self):
"""get_denoiser_data_dir returns dir with error profiles"""
obs = get_denoiser_data_dir()
self.assertTrue(exists(obs))
self.assertTrue(exists(obs + 'FLX_error_profile.dat'))
def test_get_denoiser_data_dir(self):
"""get_denoiser_data_dir returns dir with error profiles"""
obs = get_denoiser_data_dir()
self.assertTrue(exists(obs))
self.assertTrue(exists(obs + 'FLX_error_profile.dat'))
from os import makedirs, remove
from os.path import exists
from qiime.util import get_tmp_filename
from cogent.util.misc import create_dir
from qiime.util import parse_command_line_parameters, get_options_lookup,\
make_option
from qiime.denoiser.preprocess import STANDARD_BACTERIAL_PRIMER
from qiime.denoiser.flowgram_clustering import denoise_seqs, denoise_per_sample
from qiime.denoiser.utils import files_exist, get_denoiser_data_dir,\
cat_sff_files
options_lookup = get_options_lookup()
DENOISER_DATA_DIR = get_denoiser_data_dir()
# denoiser.py
script_info = {}
script_info['brief_description'] = """Remove noise from 454 sequencing data"""
script_info[
'script_description'] = """The denoiser removes sequencing noise characteristic to pyrosequencing by flowgram clustering. For a detailed explanation of the underlying algorithm see (Reeder and Knight, Nature Methods 7(9), 2010)."""
script_info['script_usage'] = [
("",
"""Run denoiser on flowgrams in 454Reads.sff.txt with read-to-barcode mapping in seqs.fna,
put results into Outdir, log progress in Outdir/denoiser.log""",
"""%prog -i 454Reads.sff.txt -f seqs.fna -v -o Outdir"""),
("Multiple sff.txt files",
"""Run denoiser on two flowgram files in 454Reads_1.sff.txt and 454Reads_2.sff.txt
),
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__
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:
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)
from qiime.denoiser.utils import init_flowgram_file, append_to_flowgram_file,\
FlowgramContainerFile, FlowgramContainerArray, make_stats, store_mapping,\
store_clusters, read_denoiser_mapping, check_flowgram_ali_exe,\
sort_seqs_by_clustersize, get_denoiser_data_dir, get_flowgram_ali_exe,\
write_checkpoint, read_checkpoint, sort_mapping_by_size
from qiime.denoiser.cluster_utils import setup_cluster, adjust_workers,\
stop_workers, check_workers, ClientHandler,\
save_send, send_flowgram_to_socket
from qiime.denoiser.utils import write_sff_header
from qiime.denoiser.flowgram_filter import split_sff
from qiime.denoiser.preprocess import preprocess, preprocess_on_cluster,\
read_preprocessed_data
DENOISER_DATA_DIR = get_denoiser_data_dir()
def compute_workload(num_cores, num_flows, spread):
"""Compute workload for each individual worker
num_flows: total number of flows to be processed
num_cores: total number of workers available for processing the flows
spread: relative performance of the each worker, with 1.0 being nominal processing rate
"""
# sigma is the sum of the normalized processing velocity scores
# for each cluster processor. In a perfect world, sigma == num_cores
# and the normalized processing velocity (in spread) == 1.0
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: