def test_default_start_stop():
# Whether start or end is "." or None, attribute should always be None and
# printing should show "."
c = ['.', None]
for i1 in c:
for i2 in c:
f = feature.Feature(start=i1, end=i2)
assert f.start is None
assert f.end is None
assert f.stop is None
assert str(f) == ". . . . . . . . ", str(f)
# Make sure zero works (protects against sloppy "if start:")
f = feature.Feature(start=0, end=0)
assert f.start == f.end == f.stop == 0
assert str(f) == ". . . 0 0 . . . ", str(f)
def test_attributes_representations():
# These different ways of supplying attributes should yield identical
# results:
s = ". . . . . . . . ID=asdf"
for item in ('{"ID": ["asdf"]}', dict(ID=["asdf"]), "ID=asdf"):
result = str(feature.Feature(attributes=item))
assert result == s, result
def derived_feature_generator():
"""
Generator of items from the file that was just created...
"""
keys = ['parent', 'seqid', 'start', 'end', 'strand',
'featuretype', 'bin', 'attributes']
for line in open(fout.name):
d = dict(list(zip(keys, line.strip().split('\t'))))
d.pop('parent')
d['score'] = '.'
d['source'] = 'gffutils_derived'
d['frame'] = '.'
d['extra'] = []
d['attributes'] = helpers._unjsonify(d['attributes'])
f = feature.Feature(**d)
f.id = self._id_handler(f)
yield f
def _candidate_merges(self, f):
"""
Identifies those features that originally had the same ID as `f`
(according to the id_spec), but were modified because of duplicate
IDs.
"""
candidates = [self._get_feature(f.id)]
c = self.conn.cursor()
results = c.execute(
constants._SELECT + '''
JOIN duplicates ON
duplicates.newid = features.id WHERE duplicates.idspecid = ?''',
(f.id, ))
for i in results:
candidates.append(
feature.Feature(dialect=self.iterator.dialect, **i))
return list(set(candidates))
def _get_feature(self, ID):
c = self.conn.cursor()
results = c.execute(
constants._SELECT + ' WHERE id = ?', (ID,)).fetchone()
return feature.Feature(dialect=self.iterator.dialect, **results)
def test_default_feature():
# Default Feature is 8 tab-delimited ".", with a trailing tab
assert str(feature.Feature()) == \
". . . . . . . . "