def test_classify(self):
# simplest gotu workflow
input_fp = join(self.datdir, 'align', 'bowtie2')
samples, files, demux = parse_samples(input_fp)
mapper, chunk = build_mapper()
ranks = ['none']
obs = classify(mapper, files, samples=samples, demux=demux,
ranks=ranks, chunk=chunk)['none']
self.assertEqual(obs['S01']['G000011545'], 48)
self.assertNotIn('G000007145', obs['S02'])
self.assertEqual(obs['S03']['G000009345'], 640)
self.assertEqual(obs['S04']['G000240185'], 4)
self.assertEqual(obs['S05']['G000191145'], 10)
# complex genus/process stratification workflow
input_fp = join(self.datdir, 'align', 'burst')
coords_fp = join(self.datdir, 'function', 'coords.txt.xz')
map_fps = [join(self.datdir, 'function', 'uniref.map.xz'),
join(self.datdir, 'function', 'go', 'process.tsv.xz')]
strata_dir = join(self.datdir, 'output', 'burst.genus.map')
samples, files, demux = parse_samples(input_fp)
tree, rankdic, namedic, root = build_hierarchy(
map_fps=map_fps, map_as_rank=True)
mapper, chunk = build_mapper(coords_fp=coords_fp, overlap=80)
stratmap = parse_strata(strata_dir, samples)
obs = classify(
mapper, files, samples=samples, demux=demux, tree=tree,
rankdic=rankdic, namedic=namedic, root=root, stratmap=stratmap,
chunk=chunk, ranks=['process'])['process']
self.assertEqual(obs['S01'][('Thermus', 'GO:0005978')], 2)
self.assertEqual(obs['S02'][('Bacteroides', 'GO:0006814')], 1)
self.assertEqual(obs['S03'][('Escherichia', 'GO:0006813')], 2)
self.assertEqual(len(obs['S04']), 39)
def test_parse_strata(self):
# default
for i in range(1, 4):
open(join(self.tmpdir, f'S{i}.txt'), 'a').close()
obs = parse_strata(self.tmpdir)
exp = {f'S{i}': join(self.tmpdir, f'S{i}.txt') for i in range(1, 4)}
self.assertDictEqual(obs, exp)
# with sample Ids
obs = parse_strata(self.tmpdir, samples=['S1', 'S2'])
exp = {f'S{i}': join(self.tmpdir, f'S{i}.txt') for i in range(1, 3)}
self.assertDictEqual(obs, exp)
# sample missing
with self.assertRaises(ValueError) as ctx:
parse_strata(self.tmpdir, samples=['S1', 'S2', 'Sx'])
self.assertEqual(str(ctx.exception), (
'Cannot locate stratification files for one or more samples.'))