def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args, default_iter_step=None)
if self.iter_range.iter_step is None:
#use about 10 blocks by default
self.iter_range.iter_step = max(
1,
(self.iter_range.iter_stop - self.iter_range.iter_start) // 10)
self.output_filename = args.output
self.assignments_filename = args.assignments
self.kinetics_filename = args.kinetics
self.mcbs_alpha = args.alpha
self.mcbs_acalpha = args.acalpha if args.acalpha else self.mcbs_alpha
self.mcbs_nsets = args.nsets if args.nsets else mclib.get_bssize(
self.mcbs_alpha)
self.evolution_mode = args.evolution_mode
self.evol_window_frac = args.window_frac
if self.evol_window_frac <= 0 or self.evol_window_frac > 1:
raise ValueError(
'Parameter error -- fractional window defined by --window-frac must be in (0,1]'
)
def process_args(self, args):
self.data_reader.process_args(args)
self.data_reader.open()
self.iter_range.data_manager = self.data_reader
self.iter_range.process_args(args)
self.output_h5file = h5py.File(args.output, 'w')
self.alpha = args.alpha
self.autocorrel_alpha = args.acalpha or self.alpha
self.n_sets = args.nsets or mclib.get_bssize(self.alpha)
self.do_evol = args.do_evol
self.evol_step = args.evol_step or 1
def process_args(self, args):
self.data_reader.process_args(args)
self.data_reader.open()
self.iter_range.data_manager = self.data_reader
self.iter_range.process_args(args)
self.output_h5file = h5py.File(args.output, 'w')
self.alpha = args.alpha
self.autocorrel_alpha = args.acalpha or self.alpha
self.n_sets = args.nsets or mclib.get_bssize(self.alpha)
self.do_evol = args.do_evol
self.evol_step = args.evol_step or 1
def process_args(self, args):
self.kinetics_filename = args.kinetics
# Disable the bootstrap or the correlation analysis.
self.mcbs_enable = args.bootstrap if args.bootstrap is not None else True
self.do_correl = args.correl if args.correl is not None else True
self.mcbs_alpha = args.alpha
self.mcbs_acalpha = args.acalpha if args.acalpha else self.mcbs_alpha
self.mcbs_nsets = args.nsets if args.nsets else mclib.get_bssize(self.mcbs_alpha)
self.display_averages = args.display_averages
self.evolution_mode = args.evolution_mode
self.evol_window_frac = args.window_frac
if self.evol_window_frac <= 0 or self.evol_window_frac > 1:
raise ValueError('Parameter error -- fractional window defined by --window-frac must be in (0,1]')
def process_args(self, args):
self.kinetics_filename = args.kinetics
# Disable the bootstrap or the correlation analysis.
self.mcbs_enable = args.bootstrap if args.bootstrap is not None else True
self.do_correl = args.correl if args.correl is not None else True
self.mcbs_alpha = args.alpha
self.mcbs_acalpha = args.acalpha if args.acalpha else self.mcbs_alpha
self.mcbs_nsets = args.nsets if args.nsets else mclib.get_bssize(self.mcbs_alpha)
self.display_averages = args.display_averages
self.evolution_mode = args.evolution_mode
self.evol_window_frac = args.window_frac
if self.evol_window_frac <= 0 or self.evol_window_frac > 1:
raise ValueError('Parameter error -- fractional window defined by --window-frac must be in (0,1]')
def process_args(self, args):
self.data_reader.process_args(args)
self.data_reader.open()
self.iter_range.data_manager = self.data_reader
self.iter_range.process_args(args)
self.output_h5file = h5py.File(args.output, 'w')
self.alpha = args.alpha
# Disable the bootstrap or the correlation analysis.
self.mcbs_enable = args.bootstrap if args.bootstrap is not None else True
self.do_correl = args.correl if args.correl is not None else True
self.autocorrel_alpha = args.acalpha or self.alpha
self.n_sets = args.nsets or mclib.get_bssize(self.alpha)
self.do_evol = args.do_evol
self.evol_step = args.evol_step or 1
def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args, default_iter_step=None)
if self.iter_range.iter_step is None:
#use about 10 blocks by default
self.iter_range.iter_step = max(1, (self.iter_range.iter_stop - self.iter_range.iter_start) // 10)
self.output_filename = args.output
self.assignments_filename = args.assignments
self.mcbs_alpha = args.alpha
self.mcbs_acalpha = args.acalpha if args.acalpha else self.mcbs_alpha
self.mcbs_nsets = args.nsets if args.nsets else mclib.get_bssize(self.mcbs_alpha)
self.evolution_mode = args.evolution_mode
def process_args(self, args):
self.data_reader.process_args(args)
self.data_reader.open()
self.iter_range.data_manager = self.data_reader
self.iter_range.process_args(args)
self.output_h5file = h5py.File(args.output, 'w')
self.alpha = args.alpha
# Disable the bootstrap or the correlation analysis.
self.mcbs_enable = args.bootstrap if args.bootstrap is not None else True
self.do_correl = args.correl if args.correl is not None else True
self.autocorrel_alpha = args.acalpha or self.alpha
self.n_sets = args.nsets or mclib.get_bssize(self.alpha)
self.do_evol = args.do_evol
self.evol_step = args.evol_step or 1
def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args, default_iter_step=None)
if self.iter_range.iter_step is None:
#use about 10 blocks by default
self.iter_range.iter_step = max(
1,
(self.iter_range.iter_stop - self.iter_range.iter_start) // 10)
self.output_filename = args.output
self.assignments_filename = args.assignments
self.mcbs_alpha = args.alpha
self.mcbs_acalpha = args.acalpha if args.acalpha else self.mcbs_alpha
self.mcbs_nsets = args.nsets if args.nsets else mclib.get_bssize(
self.mcbs_alpha)
self.evolution_mode = args.evolution_mode
def process_args(self, args):
self.progress.process_args(args)
self.data_reader.process_args(args)
with self.data_reader:
self.iter_range.process_args(args, default_iter_step=None)
if self.iter_range.iter_step is None:
#use about 10 blocks by default
self.iter_range.iter_step = max(1, (self.iter_range.iter_stop - self.iter_range.iter_start) // 10)
self.output_filename = args.output
self.assignments_filename = args.assignments
self.kinetics_filename = args.kinetics
self.mcbs_alpha = args.alpha
self.mcbs_acalpha = args.acalpha if args.acalpha else self.mcbs_alpha
self.mcbs_nsets = args.nsets if args.nsets else mclib.get_bssize(self.mcbs_alpha)
self.evolution_mode = args.evolution_mode
self.evol_window_frac = args.window_frac
if self.evol_window_frac <= 0 or self.evol_window_frac > 1:
raise ValueError('Parameter error -- fractional window defined by --window-frac must be in (0,1]')
