def __init__(self, args):
self.args = args
self.path = check_path(args.get('--prefix', None))
self.prefix = check_prefix(args.get('--prefix', None))
self.dataset = "%s.modified" % self.prefix if self.path is None else "%s.modified" % (
self.path / self.prefix)
self.threads = int(args.get('--threads'))
self.variants_file = check_file(args.get('--variants_h5', None))
self.max_missing = int(args.get('--max_missing'))
self.max_multiallelic = int(args.get('--max_multiallelic'))
def __init__(self, args):
# initial user parameters
self.mode = None
self.model_file = check_file(args.get('--model', None))
self.model_name = pathlib.Path(args['--model']).name
self.time = float(
args['--time']) if not args['--time'] is None else None
self.time_low = float(
args['--time_low']) if not args['--time_low'] is None else None
self.time_high = float(
args['--time_high']) if not args['--time_high'] is None else None
self.theta = float(
args['--theta']) if not args['--theta'] is None else None
self.theta_low = float(
args['--theta_low']) if not args['--theta_low'] is None else None
self.theta_high = float(
args['--theta_high']) if not args['--theta_high'] is None else None
self.migration = float(
args['--migration']) if not args['--migration'] is None else None
self.migration_low = float(
args['--migration_low']
) if not args['--migration_low'] is None else None
self.migration_high = float(
args['--migration_high']
) if not args['--migration_high'] is None else None
self.derived_coalescence = float(
args['--derived_Ne']) if not args['--derived_Ne'] is None else None
self.derived_coalescence_low = float(
args['--derived_low']
) if not args['--derived_low'] is None else None
self.derived_coalescence_high = float(
args['--derived_high']
) if not args['--derived_high'] is None else None
self.ancestor_population_id = args['--ancestor_population']
self.kmax = int(args['--kmax'])
self.seed = int(args['--seed'])
self.sample_file = check_file(args.get('--sample_file', None))
self.genome_file = check_file(args.get('--genome_file', None))
#self.windows_file = check_file(args['--windows_hd5']) if not args['--windows_hd5'] is None else None
self.windows_file = None
self.variants_file = check_file(
args['--variants_hd5']
) if not args['--variants_hd5'] is None else None
self.threads = int(args['--threads'])
self.path = check_path(args.get('--prefix', None))
self.prefix = check_prefix(args.get('--prefix', None))
self.dataset = self.prefix if self.path is None else (self.path /
self.prefix)
self.parameters_numeric = {}
self.parameters_symbolic = {}
self.boundaries = {}
self.check_parameters()
##########################################################
self.max_by_mutype = {mutype: self.kmax for mutype in MUTYPES}
self.mutuple_space = []
def __init__(self, args):
self.args = args
self.blocks_file = check_file(args.get('--blocks', None))
self.coordinates_file = check_file(args.get('--coordinates', None))
self.path = check_path(args.get('--prefix', None))
self.prefix = check_prefix(args.get('--prefix', None))
self.dataset = "%s.modified" % self.prefix if self.path is None else "%s.modified" % (
self.path / self.prefix)
self.threads = int(args.get('--threads'))
self.sample_file = check_file(args.get('--sample_file', None))
self.genome_file = check_file(args.get('--genome_file', None))
self.max_block_length = None
def __init__(self, args):
# initial user parameters
self.mode = None
self.model_file = check_file(args.get('--model', None))
self.model_name = pathlib.Path(args['--model']).name
self.time_MLE = float(
args['--time_MLE']) if not args['--time_MLE'] is None else None
#self.migration_MLE = float(args['--migration_MLE']) if not args['--migration_MLE'] is None else None
self.mutation_rate = float(
args['--mu']) if not args['--mu'] is None else None
self.derived_coalescence_MLE = float(
args['--derived_MLE']
) if not args['--derived_MLE'] is None else None
self.block_size = float(
args['--block_size']) if not args['--block_size'] is None else None
self.theta_low = float(
args['--theta_low']) if not args['--theta_low'] is None else None
self.theta_high = float(
args['--theta_high']) if not args['--theta_high'] is None else None
self.migration_high = float(
args['--migration_high']
) if not args['--migration_high'] is None else None
self.migration_low = float(
args['--migration_low']
) if not args['--migration_low'] is None else None
self.grid_raw_file = check_file(args.get('--grid', None))
self.ancestor_population_id = args['--ancestor_population']
self.kmax = int(args['--kmax'])
self.sample_file = check_file(args.get('--sample_file', None))
self.genome_file = check_file(args.get('--genome_file', None))
self.windows_file = check_file(
args['--windows_hd5']
) if not args['--windows_hd5'] is None else None
self.threads = int(args['--threads'])
self.path = check_path(args.get('--prefix', None))
self.prefix = check_prefix(args.get('--prefix', None))
self.dataset = self.prefix if self.path is None else (self.path /
self.prefix)
self.parameters_numeric = {}
self.parameters_symbolic = {}
self.check_parameters()
self.grid_raw = None
self.grid_gimble = None
##########################################################
self.max_by_mutype = {mutype: self.kmax for mutype in MUTYPES}
self.mutuple_space = []
self.probability_matrix_by_parameter_tuple = {}
self.window_pos_by_window_id = {}
self.x_boundaries = []
def __init__(self, args):
self.args = args
self.sample_file = check_file(args.get('--sample_file', None))
self.genome_file = check_file(args.get('--genome_file', None))
self.blocks_file = check_file(args.get('--blocks', None))
self.vcf_file = check_file(args.get('--vcf', None))
self.path = check_path(args.get('--prefix', None))
self.prefix = check_prefix(args.get('--prefix', None))
self.dataset = self.prefix if self.path is None else (self.path /
self.prefix)
self.threads = int(args.get('--threads'))
self.block_length = None
self.max_block_length = None
self.variant_count = 0
def __init__(self, args):
self.args = args
self.sample_file = check_file(args.get('--sample_file', None))
self.genome_file = check_file(args.get('--genome_file', None))
self.blocks_file = check_file(args.get('--blocks_h5', None))
self.variants_file = check_file(args.get('--variants_h5', None))
self.path = check_path(args.get('--prefix', None))
self.prefix = check_prefix(args.get('--prefix', None))
self.dataset = self.prefix if self.path is None else (self.path /
self.prefix)
self.window_size = int(args.get('--window_size'))
self.overlap = int(args.get('--overlap'))
self.max_block_distance = int(args.get('--max_block_distance'))
self.threads = int(args.get('--threads'))
self.block_length = None
self.max_block_length = None
def __init__(self, args):
self.model_file = check_file(args.get('--model', None))
self.zarr_store = None
self.time = float(
args['--time']) if not args['--time'] is None else None
self.theta = float(
args['--theta']) if not args['--theta'] is None else None
self.migration = float(
args['--migration']) if not args['--migration'] is None else None
'''
self.pop_ids = 'A,B,A&B'
self.pop_Ns = '1.2,1.2,1.4'
slef
'''
self.derived_coalescence = float(
args['--derived_Ne']) if not args['--derived_Ne'] is None else None
self.kmax = int(args['--kmax'])
self.seed = int(args['--seed'])
self.sample_file = check_file(args.get('--sample_file', None))
self.genome_file = check_file(args.get('--genome_file', None))
#self.windows_file = check_file(args['--windows_hd5']) if not args['--windows_hd5'] is None else None
self.windows_file = None
self.variants_file = check_file(
args['--variants_hd5']
) if not args['--variants_hd5'] is None else None
self.threads = int(args['--threads'])
self.path = check_path(args.get('--prefix', None))
self.prefix = check_prefix(args.get('--prefix', None))
self.dataset = self.prefix if self.path is None else (self.path /
self.prefix)
self.parameters_numeric = {}
self.parameters_symbolic = {}
self.boundaries = {}
self.check_parameters()
##########################################################
self.max_by_mutype = {mutype: self.kmax for mutype in MUTYPES}
self.mutuple_space = []
def __init__(self, args):
self.args = args
self.sample_file = check_file(args.get('--sample_file', None))
self.genome_file = check_file(args.get('--genome_file', None))
self.bed_file = check_file(args.get('--bed_file', None))
self.path = check_path(args.get('--prefix', None))
self.prefix = check_prefix(args.get('--prefix', None))
self.dataset = self.prefix if self.path is None else (self.path /
self.prefix)
self.min_samples = int(args['--min_samples'])
self.block_length = int(args['--block_length'])
self.min_interval_length = int(args['--min_interval_length'])
self.max_block_length = int(args['--max_block_span'])
if self.max_block_length < self.block_length:
sys.exit(
"[X] '--max_block_length' must be greater or equal to '--block_length'"
)
self.max_interval_distance = (self.max_block_length -
self.block_length) + 1
self.threads = int(args.get('--threads'))
self.bed_length_total = 0