def _relation(self, id, join_on, join_to, level=None, featuretype=None,
order_by=None, reverse=False, completely_within=False,
limit=None):
# The following docstring will be included in the parents() and
# children() docstrings to maintain consistency, since they both
# delegate to this method.
"""
Parameters
----------
id : string or a Feature object
level : None or int
If `level=None` (default), then return all children regardless
of level. If `level` is an integer, then constrain to just that
level.
{_method_doc}
Returns
-------
A generator object that yields :class:`Feature` objects.
"""
if isinstance(id, Feature):
id = id.id
other = '''
JOIN relations
ON relations.{join_on} = features.id
WHERE relations.{join_to} = ?
'''.format(**locals())
args = [id]
level_clause = ''
if level is not None:
level_clause = 'relations.level = ?'
args.append(level)
query, args = helpers.make_query(
args=args,
other=other,
extra=level_clause,
featuretype=featuretype,
order_by=order_by,
reverse=reverse,
limit=limit,
completely_within=completely_within,
)
# modify _SELECT so that only unique results are returned
query = query.replace("SELECT", "SELECT DISTINCT")
for i in self._execute(query, args):
yield self._feature_returner(**i)
def _relation(self, id, join_on, join_to, level=None, featuretype=None,
order_by=None, reverse=False, completely_within=False,
limit=None):
# The following docstring will be included in the parents() and
# children() docstrings to maintain consistency, since they both
# delegate to this method.
"""
Parameters
----------
id : string or a Feature object
level : None or int
If `level=None` (default), then return all children regardless
of level. If `level` is an integer, then constrain to just that
level.
{_method_doc}
Returns
-------
A generator object that yields :class:`Feature` objects.
"""
if isinstance(id, Feature):
id = id.id
other = '''
JOIN relations
ON relations.{join_on} = features.id
WHERE relations.{join_to} = ?
'''.format(**locals())
args = [id]
level_clause = ''
if level is not None:
level_clause = 'relations.level = ?'
args.append(level)
query, args = helpers.make_query(
args=args,
other=other,
extra=level_clause,
featuretype=featuretype,
order_by=order_by,
reverse=reverse,
limit=limit,
completely_within=completely_within,
)
# modify _SELECT so that only unique results are returned
query = query.replace("SELECT", "SELECT DISTINCT")
for i in self._execute(query, args):
yield self._feature_returner(**i)
def all_features(self, limit=None, strand=None, featuretype=None,
order_by=None, reverse=False, completely_within=False):
"""
Returns an iterator of all :class:`Feature` objects in the database.
Parameters
----------
{_method_doc}
"""
query, args = helpers.make_query(
args=[],
limit=limit,
strand=strand,
featuretype=featuretype,
order_by=order_by,
reverse=reverse,
completely_within=completely_within
)
for i in self._execute(query, args):
yield self._feature_returner(**i)
def features_of_type(self, featuretype, limit=None, strand=None,
order_by=None, reverse=False,
completely_within=False):
"""
Returns an iterator of :class:`gffutils.Feature` objects.
Parameters
----------
{_method_doc}
"""
query, args = helpers.make_query(
args=[],
limit=limit,
featuretype=featuretype,
order_by=order_by,
reverse=reverse,
strand=strand,
completely_within=completely_within,
)
for i in self._execute(query, args):
yield self._feature_returner(**i)
def features_of_type(self, featuretype, limit=None, strand=None,
order_by=None, reverse=False,
completely_within=False):
"""
Returns an iterator of :class:`gffutils.Feature` objects.
Parameters
----------
{_method_doc}
"""
query, args = helpers.make_query(
args=[],
limit=limit,
featuretype=featuretype,
order_by=order_by,
reverse=reverse,
strand=strand,
completely_within=completely_within,
)
for i in self._execute(query, args):
yield self._feature_returner(**i)
