def test_format_summarize_taxa(self):
"""format_summarize_taxa functions as expected"""
exp = '\n'.join(['Taxon\tfoo\tbar\tfoobar',
'a;b;c\t0\t1\t2',
'd;e;f\t3\t4\t5\n'])
obs = ''.join(list(format_summarize_taxa(self.taxa_summary, \
self.taxa_header)))
self.assertEqual(obs, exp)
def test_format_summarize_taxa(self):
"""format_summarize_taxa functions as expected"""
# Classic format.
exp = "\n".join(["Taxon\tfoo\tbar\tfoobar", "a;b;c\t0\t1\t2", "d;e;f\t3\t4\t5\n"])
obs = "".join(list(format_summarize_taxa(self.taxa_summary, self.taxa_header)))
self.assertEqual(obs, exp)
# BIOM format. Test by converting our expected output to a biom table
# and comparing that to our observed table.
exp = parse_classic_table_to_rich_table(exp.split("\n"), None, None, None, SparseTaxonTable)
obs = "".join(list(format_summarize_taxa(self.taxa_summary, self.taxa_header, file_format="biom")))
obs = parse_biom_table(obs)
self.assertEqual(obs, exp)
# Bad file_format argument.
with self.assertRaises(ValueError):
list(format_summarize_taxa(self.taxa_summary, self.taxa_header, file_format="foo"))
def test_format_summarize_taxa(self):
"""format_summarize_taxa functions as expected"""
# Classic format.
exp = '\n'.join(['Taxon\tfoo\tbar\tfoobar',
'a;b;c\t0\t1\t2',
'd;e;f\t3\t4\t5\n'])
obs = ''.join(list(format_summarize_taxa(self.taxa_summary,
self.taxa_header)))
self.assertEqual(obs, exp)
# BIOM format. Test by converting our expected output to a biom table
# and comparing that to our observed table.
exp = parse_classic_table_to_rich_table(exp.split('\n'), None, None,
None, SparseTaxonTable)
obs = ''.join(list(format_summarize_taxa(self.taxa_summary,
self.taxa_header,
file_format='biom')))
obs = parse_biom_table(obs)
self.assertEqual(obs, exp)
# Bad file_format argument.
with self.assertRaises(ValueError):
list(format_summarize_taxa(self.taxa_summary, self.taxa_header,
file_format='foo'))
