def test_bed_parser(self):
data = [
'chr20\t61724611\t61725646',
'chr20\t61304163\t61305182',
'chr20\t61286467\t61286789',
]
self.assertEqual(
list(ranges.parse_lines(data, 'bed')), [
ranges.make_range('chr20', 61724611, 61725646),
ranges.make_range('chr20', 61304163, 61305182),
ranges.make_range('chr20', 61286467, 61286789),
])
def test_bedpe_parser_skips_cross_chr_events(self):
# pylint: disable=line-too-long
data = [
'chr20\t25763416\t25765517\tchr21\t25825181\t25826882\tP2_PM_20_1549\t63266\t+\tTYPE:DELETION',
'chr20\t25972820\t25972991\tchr20\t26045347\t26045538\tP2_PM_20_696\t72548\t+\tTYPE:DELETION',
'chr20\t23719873\t23721974\tchr20\t23794822\t23796523\tP2_PM_20_1548\t76450\t+\tTYPE:DELETION',
]
self.assertEqual(
list(ranges.parse_lines(data, 'bedpe')), [
ranges.make_range('chr20', 25972820, 26045538),
ranges.make_range('chr20', 23719873, 23796523),
])
def test_unknown_filetype(self):
with self.assertRaises(ValueError):
ranges.parse_lines([], file_format='png')