def fromgff3(filename, region=None):
"""
Extract feature rows from a GFF3 file.
.. versionadded:: 0.2
.. versionchanged:: 0.15
A region query string of the form '[seqid]' or '[seqid]:[start]-[end]' may be given
for the ``region`` argument. If given, requires the GFF3 file to be bgzipped and
tabix indexed.
"""
if region is None:
# parse file as tab-delimited
tbl = fromtsv(filename)
else:
# extract via tabix
tbl = fromtabix(filename, region=region)
return convertgff3(tbl)
def fromgff3(filename):
"""
Extract feature rows from a GFF3 file.
.. versionadded:: 0.2
"""
# parse file as tab-delimited
t0 = fromtsv(filename)
# push header
t1 = pushheader(t0, ('seqid', 'source', 'type', 'start', 'end', 'score', 'strand', 'phase', 'attributes'))
# skip comments
t2 = skipcomments(t1, '#')
# ignore any row not 9 values long (e.g., trailing fasta)
t3 = rowlenselect(t2, 9)
# parse attributes into a dict
t4 = convert(t3, 'attributes', gff3_parse_attributes)
# parse coordinates
t5 = convert(t4, ('start', 'end'), int)
return HybridRowView(t5)
def test_totsv():
t = [('fruit', 'city', 'sales'), ('orange', 'London', '12'),
('banana', 'London', '42'), ('orange', 'Paris', '31'),
('banana', 'Amsterdam', '74'), ('kiwi', 'Berlin', '55')]
f = NamedTemporaryFile(delete=False)
p = totsv(f.name)
p.push(t)
ieq(t, fromtsv(f.name))
def test_totsv():
t = [('fruit', 'city', 'sales'),
('orange', 'London', '12'),
('banana', 'London', '42'),
('orange', 'Paris', '31'),
('banana', 'Amsterdam', '74'),
('kiwi', 'Berlin', '55')]
f = NamedTemporaryFile(delete=False)
p = totsv(f.name)
p.push(t)
iassertequal(t, fromtsv(f.name))
def test_totsv():
t = [
("fruit", "city", "sales"),
("orange", "London", "12"),
("banana", "London", "42"),
("orange", "Paris", "31"),
("banana", "Amsterdam", "74"),
("kiwi", "Berlin", "55"),
]
f = NamedTemporaryFile(delete=False)
p = totsv(f.name)
p.push(t)
ieq(t, fromtsv(f.name))
