Skip to content

Commit

Permalink
update the docstring to refer to splice sites everywhere instead of i…
Browse files Browse the repository at this point in the history
…ntrons
  • Loading branch information
Juke34 committed Jul 4, 2023
1 parent 1e6010e commit 5778b4e
Showing 1 changed file with 10 additions and 10 deletions.
20 changes: 10 additions & 10 deletions gffutils/interface.py
Original file line number Diff line number Diff line change
Expand Up @@ -1280,37 +1280,37 @@ def create_splice_sites(
numeric_sort=False,
):
"""
Create introns from existing annotations.
Create splice sites from existing annotations.
Parameters
----------
exon_featuretype : string
Feature type to use in order to infer introns. Typically `"exon"`.
Feature type to use in order to infer splice sites. Typically `"exon"`.
grandparent_featuretype : string
If `grandparent_featuretype` is not None, then group exons by
children of this featuretype. If `granparent_featuretype` is
"gene" (default), then introns will be created for all first-level
"gene" (default), then splice sites will be created for all first-level
children of genes. This may include mRNA, rRNA, ncRNA, etc. If
you only want to infer introns from one of these featuretypes
you only want to infer splice sites from one of these featuretypes
(e.g., mRNA), then use the `parent_featuretype` kwarg which is
mutually exclusive with `grandparent_featuretype`.
parent_featuretype : string
If `parent_featuretype` is not None, then only use this featuretype
to infer introns. Use this if you only want a subset of
featuretypes to have introns (e.g., "mRNA" only, and not ncRNA or
to infer splice sites. Use this if you only want a subset of
featuretypes to have splice sites (e.g., "mRNA" only, and not ncRNA or
rRNA). Mutually exclusive with `grandparent_featuretype`.
merge_attributes : bool
Whether or not to merge attributes from all exons. If False then no
attributes will be created for the introns.
attributes will be created for the splice sites.
numeric_sort : bool
If True, then merged attributes that can be cast to float will be
sorted by their numeric values (but will still be returned as
string). This is useful, for example, when creating introns between
string). This is useful, for example, when creating splice sites between
exons and the exons have exon_number attributes as an integer.
Using numeric_sort=True will ensure that the returned exons have
merged exon_number attribute of ['9', '10'] (numerically sorted)
Expand All @@ -1319,15 +1319,15 @@ def create_splice_sites(
Returns
-------
A generator object that yields :class:`Feature` objects representing
new introns
new splice sites
Notes
-----
The returned generator can be passed directly to the
:meth:`FeatureDB.update` method to permanently add them to the
database, e.g., ::
db.update(db.create_introns())
db.update(db.create_splice sites())
"""
if (grandparent_featuretype and parent_featuretype) or (
Expand Down

0 comments on commit 5778b4e

Please sign in to comment.