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#!/usr/bin/env python
# -----------------------------------------------------------------------------
# Copyright (c) 2011-2017, The BIOM Format Development Team.
#
# Distributed under the terms of the Modified BSD License.
#
# The full license is in the file COPYING.txt, distributed with this software.
# -----------------------------------------------------------------------------
from unittest import TestCase, main
import os
import biom
from biom.cli.table_normalizer import _normalize_table
from biom.exception import UnknownAxisError
class TableNormalizerTests(TestCase):
def setUp(self):
"""initialize objects for use in tests"""
self.cmd = _normalize_table
cwd = os.getcwd()
if os.path.sep in __file__:
os.chdir(os.path.dirname(__file__))
self.table = biom.load_table(os.path.join('test_data', 'test.json'))
os.chdir(cwd)
def test_bad_inputs(self):
# relative_abund and pa
with self.assertRaises(ValueError):
self.cmd(self.table, relative_abund=True,
presence_absence=True, axis="sample")
# no normalization type
with self.assertRaises(ValueError):
self.cmd(self.table, relative_abund=False,
presence_absence=False, axis="sample")
# bad axis
with self.assertRaises(UnknownAxisError):
self.cmd(self.table, relative_abund=True,
axis="nonsense")
if __name__ == "__main__":
main()
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