______________________________________________________________________________________ test_roundtrip _______________________________________________________________________________________
def test_roundtrip():
"""
Feature -> SeqFeature -> Feature should be invariant.
"""
db_fname = gffutils.example_filename("gff_example1.gff3")
db = gffutils.create_db(db_fname, ":memory:")
feature = db["ENSMUSG00000033845"]
feature.keep_order = True
dialect = feature.dialect
> s = bp.to_seqfeature(feature)
gffutils/test/test_biopython_integration.py:15:
_ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _ _
feature = <Feature gene (chr1:4763287-4775820[-]) at 0xbc359633390>
def to_seqfeature(feature):
"""
Converts a gffutils.Feature object to a Bio.SeqFeature object.
The GFF fields `source`, `score`, `seqid`, and `frame` are stored as
qualifiers. GFF `attributes` are also stored as qualifiers.
Parameters
----------
feature : Feature object, or string
If string, assume it is a GFF or GTF-format line; otherwise just use
the provided feature directly.
"""
if isinstance(feature, str):
feature = feature_from_line(feature)
qualifiers = {
"source": [feature.source],
"score": [feature.score],
"seqid": [feature.seqid],
"frame": [feature.frame],
}
qualifiers.update(feature.attributes)
> return SeqFeature(
# Convert from GFF 1-based to standard Python 0-based indexing used by
# BioPython
FeatureLocation(
feature.start - 1, feature.stop, strand=_biopython_strand[feature.strand]
),
id=feature.id,
type=feature.featuretype,
qualifiers=qualifiers,
)
E NameError: name 'SeqFeature' is not defined
gffutils/biopython_integration.py:46: NameError
Version: 0.13
Python-3.11
FreeBSD 14.1