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 test_fromtabix():
actual = fromtabix('fixture/test.bed.gz', region='Pf3D7_02_v3:110000-120000')
expect = (('#chrom', 'start', 'end', 'region'),
('Pf3D7_02_v3', '105800', '447300', 'Core'))
ieq(expect, actual)
def test_fromtabix_noheader():
actual = fromtabix('fixture/test_noheader.bed.gz', region='Pf3D7_02_v3:110000-120000')
expect = (('Pf3D7_02_v3', '105800', '447300', 'Core'),)
ieq(expect, actual)
def test_fromtabix():
actual = fromtabix('fixture/test.bed.gz',
region='Pf3D7_02_v3:110000-120000')
expect = (('#chrom', 'start', 'end', 'region'), ('Pf3D7_02_v3', '105800',
'447300', 'Core'))
ieq(expect, actual)
def test_fromtabix_noheader():
actual = fromtabix('fixture/test_noheader.bed.gz',
region='Pf3D7_02_v3:110000-120000')
expect = (('Pf3D7_02_v3', '105800', '447300', 'Core'), )
ieq(expect, actual)
