docs: add default values to docstring numpy style
@@ -78,7 +78,7 @@ class TreeAnc(object):
GTR model object. If string passed, it is interpreted as the type of
the GTR model. A new GTR instance will be created for this type.
- fill_overhangs : bool
+ fill_overhangs : bool, default True
In some cases, the missing data on both ends of the alignment is
filled with the gap sign('-'). If set to True, the end-gaps are converted to "unknown"
characters ('N' for nucleotides, 'X' for aminoacids). Otherwise, the alignment is treated as-is
@@ -86,14 +86,14 @@ class TreeAnc(object):
ref : None, optional
Reference sequence used in VCF mode
- verbose : int
+ verbose : int, default 3
Verbosity level as number from 0 (lowest) to 10 (highest).
- ignore_gaps : bool
+ ignore_gaps : bool, default True
Ignore gaps in branch length calculations
- convert_upper : bool, optional
- Description
+ convert_upper : bool, default True
+ Convert all sequences to upper case
seq_multiplicity : dict
If individual nodes in the tree correspond to multiple sampled sequences
@@ -101,7 +101,7 @@ class TreeAnc(object):
specified as a dictionary. This currently only affects rooting and
can be used to weigh individual tips by abundance or important during root search.
- compress : bool, optional
+ compress : bool, default True
reduce identical alignment columns to one (not useful when
inferring site specific GTR models).
@@ -335,7 +335,7 @@ class TreeAnc(object):
Returns
-------
float
- inverse of the uncompressed sequene length - length scale for short branches
+ inverse of the uncompressed sequence length - length scale for short branches
"""
return 1.0/self.data.full_length if self.data.full_length else np.nan
