#!env python
import click
from logtools import set_logging, get_logger
from bricolage.stats import (
StatsFitness, StatsVisitor, StatsMutualInformation, StatsRelevantControl,
StatsLag, StatsRobustness, StatsGenerations, StatsBindings,
StatsEnvironmental)
from experiment import ExperimentError
from bricolage.graph_maker import GraphType
log = get_logger()
class NS(object):
"""Just a namespace"""
experiment = None
def run_from_commandline(exp):
"""Assign the global experiment, and then run the commands using click"""
NS.experiment = exp
bricolage()
@click.group(chain=True)
def bricolage():
pass
verbose_ = click.option('--verbose', is_flag=True, default=False,
help="Show debug output.")
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details. You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# PartitionFinder also includes the PhyML program, the RAxML program, and the
# PyParsing library, all of which are protected by their own licenses and
# conditions, using PartitionFinder implies that you agree with those licences
# and conditions as well.
import logtools
import pandas as pd
import os
import collections
log = logtools.get_logger()
from util import PartitionFinderError
_available_lists = ["ALL", # all models, excluding those with base frequencies estimated by ML and protein GTR models
"ALLX", # all models, including those with base frequencies estimated by ML and protein GTR models
"BEAST", # all models available in BEAST 2
"MRBAYES", # all models available in MrBayes 3.3
"GAMMA", # only models with gamma distributed rates only (i.e. +G, not +I+G, not free-rates models like LG4X)
"GAMMAI", # only modles with +I+G
]
def load_models(the_config):
HERE = os.path.abspath(os.path.dirname(__file__))
the_config.all_models = pd.read_csv(os.path.join(HERE, 'models.csv'))
# Foundation, either version 3 of the License, or (at your option) any later
# version.
#
# This program is distributed in the hope that it will be useful, but WITHOUT
# ANY WARRANTY; without even the implied warranty of MERCHANTABILITY or FITNESS
# FOR A PARTICULAR PURPOSE. See the GNU General Public License for more
# details. You should have received a copy of the GNU General Public License
# along with this program. If not, see <http://www.gnu.org/licenses/>.
# PartitionFinder also includes the PhyML program, the RAxML program, and the
# PyParsing library, all of which are protected by their own licenses and
# conditions, using PartitionFinder implies that you agree with those licences
# and conditions as well.
import logtools
log = logtools.get_logger()
import subset_ops
import submodels
from util import PartitionFinderError, get_aic, get_aicc, get_bic
class SchemeError(PartitionFinderError):
pass
class SchemeResult(object):
def __init__(self, sch, nseq, branchlengths, model_selection):
self.scheme_name = sch.name
self.scheme = sch