def test_read(self):
expected = {
'GCF_005435136.1':
['d__D', 'p__P', 'c__C', 'f__F', 'g__G', 's__S1'],
'2': ['d__D', 'p__P', 'c__C', 'f__F', 'g__G', 's__S2']
}
path_tax = os.path.join(self.dir_tmp, 'tax_file.tsv')
with open(path_tax, 'w') as f:
for k, v in expected.items():
f.write(f'{k}\t{";".join(v)}\n')
t = Taxonomy()
result = t.read(path_tax)
self.assertDictEqual(expected, result)
def test_read_canonical(self):
to_write = {
'GCF_005435136.1':
['d__D', 'p__P', 'c__C', 'f__F', 'g__G', 's__S1'],
'RS_GCF_005435135.1':
['d__D', 'p__P', 'c__C', 'f__F', 'g__G', 's__S2']
}
expected = {
'G005435136': to_write['GCF_005435136.1'],
'G005435135': to_write['RS_GCF_005435135.1'],
}
path_tax = os.path.join(self.dir_tmp, 'tax_file.tsv')
with open(path_tax, 'w') as f:
for k, v in to_write.items():
f.write(f'{k}\t{";".join(v)}\n')
t = Taxonomy()
result = t.read(path_tax, canonical_ids=True)
self.assertDictEqual(expected, result)
