import sys
import os
import re
import glob
from configobj import ConfigObj
from pymsbayes import config
from pymsbayes.utils import probability
from pymsbayes.utils import functions
from pymsbayes.fileio import process_file_arg, expand_path
from pymsbayes.utils import stats
from pymsbayes.utils import parsing
from pymsbayes.utils.messaging import get_logger
_LOG = get_logger(__name__)
def get_partitions_from_posterior_sample_file(file_obj,
integer_partitions=False):
post = parsing.parse_parameters(file_obj)
if not 'taus' in post:
name = getattr(file_obj, 'name', file_obj)
raise Exception('posterior sample in {0} does not contain a '
'divergence time vector'.format(name))
if integer_partitions:
return stats.IntegerPartitionCollection(post['taus'])
return stats.PartitionCollection(post['taus'])
def parse_omega_results_file(file_obj):
"""
import unittest
import os
import sys
from pymsbayes import workers, fileio, manager
from pymsbayes.config import MsBayesConfig
from pymsbayes.test.support import package_paths
from pymsbayes.test.support.pymsbayes_test_case import PyMsBayesTestCase
from pymsbayes.utils import ToolPathManager, MSBAYES_SORT_INDEX
from pymsbayes.utils import parsing, stats
# from pymsbayes.test.test_dmc import DmcTestCase
from pymsbayes.utils.messaging import get_logger
_LOG = get_logger(__name__, level="INFO")
class ToolTestCase(PyMsBayesTestCase):
def setUp(self):
self.set_up()
self.cfg_path = package_paths.data_path('negros_panay.cfg')
self.new_cfg_path = package_paths.data_path('negros_panay_new.cfg')
self.sum_stats_path = package_paths.data_path(
'negros_panay_sum_stats_sort0.txt')
self.prior_path = package_paths.data_path(
'negros_panay_new_prior_sample_10.txt')
self.posterior_path = package_paths.data_path(
'posterior-sample.txt.gz')
def tearDown(self):
#! /usr/bin/env python
import os
import sys
from gzip import GzipFile
from __builtin__ import file
from __builtin__ import open as fopen
from pymsbayes.utils.messaging import get_logger
_LOG = get_logger(__name__)
def expand_path(path):
return os.path.abspath(os.path.expandvars(os.path.expanduser(path)))
def open(*args, **kwargs):
return FileStream(*args, **kwargs)
def process_file_arg(file_arg, mode='rU', compresslevel = None):
if isinstance(file_arg, str):
fp = expand_path(file_arg)
gzipped = False
if os.path.isfile(fp):
gzipped = is_gzipped(fp)
if compresslevel:
return GzipFileStream(fp, mode.strip('U+') + 'b',
compresslevel), True
elif gzipped:
return GzipFileStream(fp, mode.strip('U+') + 'b'), True
else:
"""
import unittest
import os
import sys
from pymsbayes import workers, fileio, manager
from pymsbayes.config import MsBayesConfig
from pymsbayes.test.support import package_paths
from pymsbayes.test.support.pymsbayes_test_case import PyMsBayesTestCase
from pymsbayes.utils import ToolPathManager, MSBAYES_SORT_INDEX
from pymsbayes.utils import parsing, stats
# from pymsbayes.test.test_dmc import DmcTestCase
from pymsbayes.utils.messaging import get_logger
_LOG = get_logger(__name__, level = "INFO")
class ToolTestCase(PyMsBayesTestCase):
def setUp(self):
self.set_up()
self.cfg_path = package_paths.data_path('negros_panay.cfg')
self.new_cfg_path = package_paths.data_path('negros_panay_new.cfg')
self.sum_stats_path = package_paths.data_path(
'negros_panay_sum_stats_sort0.txt')
self.prior_path = package_paths.data_path(
'negros_panay_new_prior_sample_10.txt')
self.posterior_path = package_paths.data_path(
'posterior-sample.txt.gz')
def tearDown(self):