def __init__(self, **kw):
PhyltrCommand.__init__(self, **kw)
self.tree_count = 0
self.taxa_count = 0
self.ultrametric = True
self.topologically_unique_trees = []
self.tree_ages = []
def __init__(self, rename=None, **kw):
PhyltrCommand.__init__(self, **kw)
if rename:
self.rename = rename
elif self.opts.filename and self.opts.from_ and self.opts.to_:
self.read_rename_file(self.opts.filename, self.opts.from_, self.opts.to_)
else:
raise ValueError("Must supply renaming dictionary or filename and columns!")
def __init__(self, dummy=False, **kw):
PhyltrCommand.__init__(self, **kw)
self.dummy = dummy
if not self.dummy: # pragma: no cover
# Setup TreeStyle
self.ts = TreeStyle()
self.ts.show_scale = False
self.ts.show_branch_support = not self.opts.no_support
self.ts.show_leaf_name = False
def __init__(self, **kw):
PhyltrCommand.__init__(self, **kw)
self.annotations = {}
if self.opts.extract and (self.opts.filename == "-"
or not self.opts.filename):
# If we're writing an extracted CSV to stdin, we don't want to also
# serialise the trees, so plumb to null
self.sink = NullSink
if not self.opts.extract:
self.read_annotation_file()
def __init__(self, **kw):
PhyltrCommand.__init__(self, **kw)
if not (self.opts.taxa or self.opts.filename):
raise ValueError(
"Must provide a list of taxa or a file containing such a list!"
)
if not self.opts.taxa:
self.opts.taxa = read_taxa(self.opts.filename,
column=self.opts.column)
self.opts.taxa = set(self.opts.taxa)
if len(self.opts.taxa) == 1:
raise ValueError("Must specify more than one taxon!")
def __init__(self, **kw):
PhyltrCommand.__init__(self, **kw)
if not (self.opts.taxa or self.opts.filename):
raise ValueError(
"Must provide a list of taxa or a file containing such a list!"
)
if not self.opts.taxa:
self.opts.taxa = read_taxa(self.opts.filename,
column=self.opts.column)
# FIXME: read_taxa returns a set, we do need an ordered data structure!
self.opts.taxa = {taxon: t for t, taxon in enumerate(self.opts.taxa)}
self.median_cache = {}
if len(self.opts.taxa) == 1:
raise ValueError("Must specify more than one taxon!")
def __init__(self, **kw):
PhyltrCommand.__init__(self, **kw)
...
def __init__(self, **kw):
PhyltrCommand.__init__(self, **kw)
self.condition = selector_from_taxa_spec(self.opts)
Command specific help is availble via "phyltr <command> --help".
"""
import os.path
import shlex
from signal import signal, SIGPIPE, SIG_DFL
import sys
from textwrap import shorten
# import all commands:
from phyltr.commands import * # noqa: F401, F403
from phyltr.commands.base import PhyltrCommand
COMMANDS = {
cls.__name__.lower(): cls
for cls in PhyltrCommand.__subclasses__()
}
def _format_command_overview():
max_name = max(len(k) for k in COMMANDS)
res = []
for cmd in sorted(COMMANDS.keys()):
res.append(' {0} {1}'.format(
cmd.ljust(max_name), shorten(COMMANDS[cmd].__doc__,
77 - max_name)))
return '\n'.join(res)
def _split_string(spec_string):
spec_string = spec_string.strip()
def __init__(self, **kw):
PhyltrCommand.__init__(self, **kw)
self.trees = []
self.cp = phyltr.utils.cladeprob.CladeProbabilities()
def __init__(self, **kw):
PhyltrCommand.__init__(self, **kw)
self.taxonset = None
def __init__(self, **kw):
PhyltrCommand.__init__(self, **kw)
self.topologies = {}