def __init__(self,
data,
name="test",
workdir="analysis-mb",
clock=False,
**kwargs):
# path attributes
self._kwargs = {}
self._kwargs.update(kwargs)
# check workdir
if workdir:
workdir = os.path.abspath(os.path.expanduser(workdir))
else:
workdir = os.path.abspath(os.path.curdir)
if not os.path.exists(workdir):
os.makedirs(workdir)
# entered args
self.name = name
self.workdir = workdir
self.data = os.path.abspath(os.path.expanduser(data))
self.nexus = os.path.join(self.workdir, self.name + ".nex")
self.binary = ""
self._get_binary(self._kwargs.get("binary"))
self.params = Params()
defaults = {
"clockratepr": "lognorm(-7,0.6)",
"clockvarpr": "tk02",
"tk02varpr": "exp(1.0)",
"brlenspr": "clock:birthdeath",
"samplestrat": "diversity",
"sampleprob": "0.1",
"speciationpr": "exp(10)",
"extinctionpr": "beta(2, 200)",
"treeagepr": "offsetexp(1, 5)",
"ngen": 100000,
"nruns": "2",
"nchains": 4,
"samplefreq": 1000,
}
for i, j in defaults.items():
setattr(self.params, i, j)
# set params
for key in self._kwargs:
setattr(self.params, key, self._kwargs[key])
# attributes
self.rasync = None
self.stdout = None
self.stderr = None
# results files
self.trees = Params()
self.trees.constre = os.path.join(self.workdir,
"{}.con.tre".format(self.name))
self.trees.info = os.path.join(self.workdir,
"{}.lstat".format(self.name))
# write a mrbayes block to a copy of the NEXUS file.
cwargs = self.params.__dict__.copy()
cwargs["nexus"] = self.data
cwargs["outname"] = self.nexus
if clock:
self._nexstring = NEX_TEMPLATE_2.format(**cwargs)
else:
self._nexstring = NEX_TEMPLATE_1.format(**cwargs)
with open(self.nexus, 'w') as out:
out.write(self._nexstring)
def __init__(self,
data,
name="test",
workdir="analysis-mb",
clock=False,
**kwargs):
# path attributes
self._kwargs = {}
self._kwargs.update(kwargs)
# check workdir
if workdir:
workdir = os.path.abspath(os.path.expanduser(workdir))
else:
workdir = os.path.abspath(os.path.curdir)
if not os.path.exists(workdir):
os.makedirs(workdir)
# entered args
self.clock = clock
self.name = name
self.workdir = workdir
self.data = os.path.abspath(os.path.expanduser(data))
self.nexus = os.path.join(self.workdir, self.name + ".nex")
self.binary = ""
self._get_binary(self._kwargs.get("binary"))
self.params = Params()
defaults = {
"clockratepr": "lognorm(-7,0.6)",
"clockvarpr": "tk02",
"tk02varpr": "exp(1.0)",
"brlenspr": "clock:birthdeath",
"samplestrat": "diversity",
"sampleprob": "0.1",
"speciationpr": "exp(10)",
"extinctionpr": "beta(2, 200)",
"treeagepr": "offsetexp(1, 5)",
"ngen": 100000,
"nruns": "1",
"nchains": 4,
"samplefreq": 1000,
}
for i, j in defaults.items():
setattr(self.params, i, j)
# set params
for key in self._kwargs:
setattr(self.params, key, self._kwargs[key])
# attributes
self.rasync = None
self.stdout = None
self.stderr = None
# results files
self.trees = Params()
runs = ("" if int(self.params.nruns) < 2 else "run1.")
self.trees.constre = os.path.join(self.workdir,
"{}.nex.con.tre".format(self.name))
self.trees.posttre = os.path.join(self.workdir,
"{}.nex.{}t".format(self.name, runs))
self.trees.pstat = os.path.join(self.workdir,
"{}.nex.pstat".format(self.name))
self._write_nexus_file()
# check attribute for existing results at this name.
if self.result_files:
print(
"Existing results loaded for run [{}], see .trees attribute.".
format(len(self.result_files), self.name))
def __init__(self,
data=None,
tests=None,
newick=None,
nboots=1000,
mincov=1):
"""
ipyrad.analysis Baba Class object.
Parameters
----------
data : string or ndarray
A string path to a .loci file produced by ipyrad. Alternatively,
data can be entered as a Numpy array of float allele frequencies
with dimension (nloci, 4 or 5, maxlen). See simulation example
in the docs.
tests : dict or list of dicts
A dictionary mapping Sample names to test taxon names, e.g.,
test = {'p1': ['a', 'b'], 'p2': ['c'], 'p3': ['e'], 'p4': ['f']}.
Four taxon tests should have p1-p4 whereas five taxon tests will
used if dict keys are p1-p5. Other key names will raise an error.
The highest value name (e.g., p5) is the outgroup.
newick: str
...
Functions
---------
run()
...
generate_tests_from_tree()
...
plot()
...
"""
# check external imports
if not sys.modules.get("toytree"):
raise ImportError(_TOYTREE_IMPORT)
if not sys.modules.get("toyplot"):
raise ImportError(_TOYPLOT_IMPORT)
## parse data as (1) path to data file, or (2) ndarray
if isinstance(data, str):
self.data = os.path.realpath(data)
else:
self.data = data
if isinstance(newick, toytree.tree):
self.newick = newick.tree.write()
else:
self.newick = newick
## store tests, check for errors
self.tests = tests
## parameters
self.params = Params()
self.params.mincov = mincov
self.params.nboots = nboots
self.params.quiet = False
self.params.database = None
## results storage
self.results_table = None
self.results_boots = None
def __init__(
self,
data,
name="test",
workdir="analysis-mb",
clock_model=False,
constraints=None,
**kwargs):
# path attributes
self._kwargs = {}
self._kwargs.update(kwargs)
# check workdir
if workdir:
workdir = os.path.abspath(os.path.expanduser(workdir))
else:
workdir = os.path.abspath(os.path.curdir)
if not os.path.exists(workdir):
os.makedirs(workdir)
# entered args
self.clock_model = clock_model
self.constraints = constraints
self.name = name
self.workdir = workdir
self.data = os.path.abspath(os.path.expanduser(data))
self.nexus = os.path.join(self.workdir, self.name + ".nex")
self.binary = ""
self._get_binary(self._kwargs.get("binary"))
self.params = Params()
defaults = {
"ngen": 100000,
"nruns": "1",
"nchains": 4,
"samplefreq": 1000,
}
if self.clock_model == 1:
defaults.update(TEMPLATE_2_DICT)
elif self.clock_model == 2:
defaults.update(TEMPLATE_3_DICT)
for i, j in defaults.items():
setattr(self.params, i, j)
# set params (overrides defaults)
for key in self._kwargs:
setattr(self.params, key, self._kwargs[key])
# attributes
self.rasync = None
self.stdout = None
self.stderr = None
# results files
self.trees = Params()
runs = ("" if int(self.params.nruns) < 2 else "run1.")
self.trees.constre = os.path.join(
self.workdir, "{}.nex.con.tre".format(self.name))
self.trees.posttre = os.path.join(
self.workdir, "{}.nex.{}t".format(self.name, runs))
self.trees.pstat = os.path.join(
self.workdir, "{}.nex.pstat".format(self.name))
self._write_nexus_file()
# check attribute for existing results at this name.
if self.result_files:
print(
"Existing results loaded for run [{}], see .trees attribute."
.format(len(self.result_files), self.name)
)