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) 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) 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) # 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)
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 = {}