def test_read_gene_coords(self):
# simple case
tbl = ('## GCF_000123456', '# NC_123456', '1 5 384', '2 410 933',
'# NC_789012', '1 912 638', '2 529 75')
obs = read_gene_coords(tbl, sort=True)
exp = {
'NC_123456': [(5, True, True, '1'), (384, False, True, '1'),
(410, True, True, '2'), (933, False, True, '2')],
'NC_789012': [(75, True, True, '2'), (529, False, True, '2'),
(638, True, True, '1'), (912, False, True, '1')]
}
self.assertDictEqual(obs, exp)
# don't sort
obs = read_gene_coords(tbl, sort=False)['NC_789012']
exp = [(638, True, True, '1'), (912, False, True, '1'),
(75, True, True, '2'), (529, False, True, '2')]
self.assertListEqual(obs, exp)
# incorrect formats
# only one column
msg = 'Cannot extract coordinates from line:'
with self.assertRaises(ValueError) as ctx:
read_gene_coords(('hello', ))
self.assertEqual(str(ctx.exception), f'{msg} "hello".')
# only two columns
with self.assertRaises(ValueError) as ctx:
read_gene_coords(('hello\t100', ))
self.assertEqual(str(ctx.exception), f'{msg} "hello\t100".')
# three columns but 3rd is string
with self.assertRaises(ValueError) as ctx:
read_gene_coords(('hello\t100\tthere', ))
self.assertEqual(str(ctx.exception), f'{msg} "hello\t100\tthere".')
# real coords file
fp = join(self.datdir, 'function', 'coords.txt.xz')
with openzip(fp) as f:
obs = read_gene_coords(f, sort=True)
self.assertEqual(len(obs), 107)
obs_ = obs['G000006745']
self.assertEqual(len(obs_), 7188)
self.assertTupleEqual(obs_[0], (372, True, True, '1'))
self.assertTupleEqual(obs_[1], (806, False, True, '1'))
self.assertTupleEqual(obs_[2], (816, True, True, '2'))
self.assertTupleEqual(obs_[3], (2177, False, True, '2'))
def test_ordinal_mapper(self):
# uses the same example as above, with some noises
coords = read_gene_coords(
('>n1', 'g1 5 29', 'g2 33 61', 'g3 65 94', 'gx 108 135'))
aln = StringIO('\n'.join(
('r1 n1 95 20 0 0 1 20 10 29 1 1',
'r2 n1 95 20 0 0 1 20 16 35 1 1',
'r3 n1 95 20 0 0 1 20 20 39 1 1',
'r4 n1 95 20 0 0 20 1 22 41 1 1',
'r5 n1 95 20 0 0 20 1 30 49 1 1', 'rx nx 95 20 0 0 1 20 1 20 1 1',
'r6 n1 95 20 0 0 1 20 49 30 1 1',
'r7 n1 95 20 0 0 25 6 79 60 1 1',
'r8 n1 95 20 0 0 1 20 84 65 1 1',
'r9 n1 95 20 0 0 1 20 95 82 1 1', 'rx nx 95 0 0 0 0 0 0 0 1 1',
'# end of file')))
obs = list(ordinal_mapper(aln, coords))[0]
exp = [('r1', 'g1'), ('r5', 'g2'), ('r6', 'g2'), ('r8', 'g3')]
self.assertListEqual(list(obs[0]), [x[0] for x in exp])
self.assertListEqual(list(obs[1]), [{x[1]} for x in exp])
# specify format
aln.seek(0)
obs = list(ordinal_mapper(aln, coords, fmt='b6o'))[0]
self.assertListEqual(list(obs[0]), [x[0] for x in exp])
self.assertListEqual(list(obs[1]), [{x[1]} for x in exp])
# specify chunk size
aln.seek(0)
obs = list(ordinal_mapper(aln, coords, n=5))
self.assertListEqual(list(obs[0][0]), [x[0] for x in exp[:2]])
self.assertListEqual(list(obs[0][1]), [{x[1]} for x in exp[:2]])
self.assertListEqual(list(obs[1][0]), [x[0] for x in exp[2:]])
self.assertListEqual(list(obs[1][1]), [{x[1]} for x in exp[2:]])
# add prefix
aln.seek(0)
obs = list(ordinal_mapper(aln, coords, prefix=True))[0]
self.assertListEqual(list(obs[0]), [x[0] for x in exp])
self.assertListEqual(list(obs[1]), [{f'n1_{x[1]}'} for x in exp])
# specify threshold
aln.seek(0)
obs = list(ordinal_mapper(aln, coords, th=0.5))[0]
exp = [('r1', 'g1'), ('r2', 'g1'), ('r3', 'g1'), ('r5', 'g2'),
('r6', 'g2'), ('r7', 'g3'), ('r8', 'g3'), ('r9', 'g3')]
self.assertListEqual(list(obs[0]), [x[0] for x in exp])
self.assertListEqual(list(obs[1]), [{x[1]} for x in exp])