# ---------------------------------------------------------------------------- # Copyright (c) 2013--, emperor development team. # # Distributed under the terms of the Modified BSD License. # # The full license is in the file LICENSE.md, distributed with this software. # ---------------------------------------------------------------------------- from __future__ import division from unittest import TestCase, main from os.path import exists, join from shutil import rmtree from tempfile import gettempdir import pandas as pd import warnings from numpy import array from numpy.testing import assert_almost_equal from emperor.util import ( preprocess_coords_file, nbinstall, validate_and_process_custom_axes, resolve_stable_url, EmperorWarning) warnings.simplefilter('always', category=EmperorWarning) class TopLevelTests(TestCase): def setUp(self): self.files_to_delete = [] self.mapping_file_data = MAPPING_FILE_DATA self.mapping_file_headers = ['SampleID', 'BarcodeSequence', 'LinkerPrimerSequence', 'Treatment', 'DOB', 'Description'] self.valid_columns = ['Treatment', 'DOB'] self.support_files_filename = gettempdir() self.support_files_filename_spaces = join( gettempdir(), 'Directory With Spaces/AndNoSpaces') # data for the custom axes, contains columns that are gradients self.mapping_file_data_gradient = MAPPING_FILE_DATA_GRADIENT self.mapping_file_headers_gradient = ['SampleID', 'Treatment', 'Time', 'Weight', 'Description'] self.coords_header = ['PC.355', 'PC.635', 'PC.636', 'PC.354'] self.coords_data = COORDS_DATA self.coords_eigenvalues = array([1, 2, 3, 4]) self.coords_pct = array([40, 30, 20, 10]) # jackknifed test data self.jk_mapping_file_headers = ['SampleID', 'C2', 'C3', 'C4'] self.jk_mapping_file_data = [['1', 'a', 'b', 'c'], ['2', 'd', 'e', 'f'], ['3', 'g', 'h', 'i']] self.jk_coords_header = [['1', '2', '3'], ['1', '2', '3'], ['1', '2', '3'], ['1', '2', '3']] self.jk_coords_data = [ array([[1.2, 0.1, -1.2], [-2.5, -4.0, 4.5]]), array([[-1.4, 0.05, 1.3], [2.6, 4.1, -4.7]]), array([[-1.5, 0.05, 1.6], [2.4, 4.0, -4.8]]), array([[-1.5, 0.05, 1.6], [2.4, 4.0, -4.8]])] self.jk_coords_eigenvalues = [ array([0.80, .11, 0.09]), array([0.76, .20, 0.04]), array([0.84, .14, 0.02]), array([0.84, .11, 0.05])] self.jk_coords_pcts = [ array([0.80, .10, 0.10]), array([0.76, .21, 0.03]), array([0.84, .11, 0.05]), array([0.84, .15, 0.01])] self.jk_mapping_file_data_gradient = MAPPING_FILE_DATA_GRADIENT self.jk_mapping_file_headers_gradient = ['SampleID', 'Treatment', 'Time', 'Weight', 'Description'] self.jk_coords_header_gradient = [ ['PC.354', 'PC.355', 'PC.635', 'PC.636'], ['PC.354', 'PC.355', 'PC.635', 'PC.636'], ['PC.354', 'PC.355', 'PC.635', 'PC.636'], ['PC.354', 'PC.355', 'PC.635', 'PC.636']] self.jk_coords_data_gradient = [ array([[1.2, 0.1, -1.2, 1.1], [-2.5, -4.0, 4.5, 0.3], [.5, -0.4, 3.5, 1.001], [0.67, 0.23, 1.01, 2.2]]), array([[1.2, 1, -0.2, 0.1], [-2.5, -4.0, 4.5, 3.2], [.5, -0.4, 3.5, 1.00], [0.57, 0.27, 0.95, 2.1]]), array([[1.0, 1, -1.2, 1.1], [-2.1, -2.0, 3.5, 0.3], [.5, 3, 3.5, 2], [0.60, 0.33, 1.3, 2.0]]), array([[1.2, 0.1, -1.2, 1.1], [-2.5, -4.0, 4.5, 0.3], [.5, -0.4, 3.5, 1.001], [0.69, 0.20, 1.01, 2.2]])] self.jk_coords_eigenvalues_gradient = [ array([0.80, .11, 0.09, 0.0]), array([0.76, .20, 0.04, 0.0]), array([0.84, .14, 0.02, 0.0]), array([0.84, .11, 0.05, 0.0])] self.jk_coords_pcts_gradient = [ array([0.80, .10, 0.10, 0.0]), array([0.76, .21, 0.03, 0.0]), array([0.84, .11, 0.05, 0.0]), array([0.84, .15, 0.01, 0])] self.broken_mapping_file_data = BROKEN_MAPPING_FILE self.broken_mapping_file_data_2_values = BROKEN_MAPPING_FILE_2_VALUES def tearDown(self): for f in self.files_to_delete: rmtree(f) def test_preprocess_coords_file(self): """Check correct processing is applied to the coords""" # case with custom axes out_coords_header, out_coords_data, out_eigenvals, out_pcts,\ out_coords_low, out_coords_high, o_clones = preprocess_coords_file( self.coords_header, self.coords_data, self.coords_eigenvalues, self.coords_pct, self.mapping_file_headers_gradient, self.mapping_file_data_gradient, ['Time']) expected_coords_data = array( [[0.03333333, -0.2, -0.1, 0.06, -0.06], [0.03333333, -0.3, 0.04, -0.1, 0.15], [0.2, 0.1, -0.1, -0.2, 0.08], [-0.3, 0.04, -0.01, 0.06, -0.34]]) self.assertEqual(out_coords_header, self.coords_header) self.assertEqual(out_coords_high, None) self.assertEqual(out_coords_low, None) assert_almost_equal(self.coords_eigenvalues, array([1, 2, 3, 4])) assert_almost_equal(self.coords_pct, array([40, 30, 20, 10])) self.assertEqual(o_clones, 0) # check each individual value because currently cogent assertEquals # fails when comparing the whole matrix at once for out_el, exp_el in zip(out_coords_data, expected_coords_data): for out_el_sub, exp_el_sub in zip(out_el, exp_el): self.assertAlmostEqual(out_el_sub, exp_el_sub) # case for jackknifing, based on qiime/tests/test_util.summarize_pcoas out_coords_header, out_coords_data, out_eigenvals, out_pcts,\ out_coords_low, out_coords_high, o_clones = preprocess_coords_file( self.jk_coords_header, self.jk_coords_data, self.jk_coords_eigenvalues, self.jk_coords_pcts, self.jk_mapping_file_headers, self.jk_mapping_file_data, jackknifing_method='sdev', pct_variation_below_one=True) self.assertEqual(out_coords_header, ['1', '2', '3']) assert_almost_equal(out_coords_data, array([[1.4, -0.0125, -1.425], [-2.475, -4.025, 4.7]])) assert_almost_equal(out_eigenvals, array([0.81, 0.14, 0.05])) assert_almost_equal(out_pcts, array([0.8, 0.1, 0.1])) self.assertEqual(o_clones, 0) # test the coords are working fine assert_almost_equal(out_coords_low, array([[-0.07071068, -0.0375, -0.10307764], [-0.04787136, -0.025, -0.07071068]])) assert_almost_equal(out_coords_high, array([[0.07071068, 0.0375, 0.10307764], [0.04787136, 0.025, 0.07071068]])) # test custom axes and jackknifed plots out_coords_header, out_coords_data, out_eigenvals, out_pcts,\ out_coords_low, out_coords_high, o_clones = preprocess_coords_file( self.jk_coords_header_gradient, self.jk_coords_data_gradient, self.jk_coords_eigenvalues_gradient, self.jk_coords_pcts_gradient, self.jk_mapping_file_headers_gradient, self.jk_mapping_file_data_gradient, custom_axes=['Time'], jackknifing_method='sdev', pct_variation_below_one=True) self.assertEqual(out_coords_header, ['PC.354', 'PC.355', 'PC.635', 'PC.636']) assert_almost_equal(out_coords_data, array([[-2.4, 1.15, 0.55, -0.95, 0.85], [0.73333333, -2.4, -3.5, 4.25, 1.025], [0.73333333, 0.5, 0.45, 3.5, 1.2505], [2.3, 0.6325, 0.2575, 1.0675, 2.125]])) assert_almost_equal(out_eigenvals, array([0.81, 0.14, 0.05, 0.])) assert_almost_equal(out_pcts, array([0.8, 0.1, 0.1, 0.])) # test the coords are working fine assert_almost_equal( out_coords_low, array([[0., -0.05, -0.25980762, -0.25, -0.25], [0., -0.1, -0.5, -0.25, -0.725], [0., -0., -0.85, -0., -0.24983344], [0., -0.0283945, -0.02809953, -0.07877976, -0.04787136]])) assert_almost_equal( out_coords_high, array([[1.00000000e-05, 5.0000000e-02, 2.59807621e-01, 2.50000000e-01, 2.50000000e-01], [1.00000000e-05, 1.0000000e-01, 5.00000000e-01, 2.50000000e-01, 7.25000000e-01], [1.00000000e-05, 0.0, 8.50000000e-01, 0.00000000e+00, 2.49833445e-01], [1.00000000e-05, 2.83945417e-02, 2.80995255e-02, 7.87797563e-02, 4.78713554e-02]])) self.assertEqual(o_clones, 0) # test that pct_variation_below_one is working out_coords_header, out_coords_data, out_eigenvals, out_pcts,\ out_coords_low, out_coords_high, o_clones = preprocess_coords_file( self.jk_coords_header_gradient, self.jk_coords_data_gradient, self.jk_coords_eigenvalues_gradient, self.jk_coords_pcts_gradient, self.jk_mapping_file_headers_gradient, self.jk_mapping_file_data_gradient, custom_axes=['Time'], jackknifing_method='sdev', pct_variation_below_one=False) self.assertEqual(out_coords_header, ['PC.354', 'PC.355', 'PC.635', 'PC.636']) assert_almost_equal( out_coords_data, array([[-2.4, 1.15, 0.55, -0.95, 0.85], [0.73333333, -2.4, -3.5, 4.25, 1.025], [0.73333333, 0.5, 0.45, 3.5, 1.2505], [2.3, 0.6325, 0.2575, 1.0675, 2.125]])) assert_almost_equal(out_eigenvals, array([0.81, 0.14, 0.05, 0.])) assert_almost_equal(out_pcts, array([80, 10, 10, 0])) def test_preprocess_coords_file_comparison(self): """Check the cases for comparisons plots and the special usages""" # shouldn't allow a comparison computation with only one file self.assertRaises( AssertionError, preprocess_coords_file, self.coords_header, self.coords_data, self.coords_eigenvalues, self.coords_pct, self.mapping_file_headers_gradient, self.mapping_file_data_gradient, None, None, True) out_coords_header, out_coords_data, out_eigenvals, out_pcts,\ out_coords_low, out_coords_high, o_clones = preprocess_coords_file( self.jk_coords_header, self.jk_coords_data, self.jk_coords_eigenvalues, self.jk_coords_pcts, self.jk_mapping_file_headers, self.jk_mapping_file_data, is_comparison=True, pct_variation_below_one=True) self.assertEqual(out_coords_header, ['1_0', '2_0', '3_0', '1_1', '2_1', '3_1', '1_2', '2_2', '3_2', '1_3', '2_3', '3_3']) assert_almost_equal( out_coords_data, array([[1.2, 0.1, -1.2], [-2.5, -4., 4.5], [-1.4, 0.05, 1.3], [2.6, 4.1, -4.7], [-1.5, 0.05, 1.6], [2.4, 4., -4.8], [-1.5, 0.05, 1.6], [2.4, 4., -4.8]])) assert_almost_equal(out_eigenvals, self.jk_coords_eigenvalues[0]) assert_almost_equal(out_pcts, self.jk_coords_pcts[0]) self.assertEqual(out_coords_low, None) self.assertEqual(out_coords_high, None) self.assertEqual(o_clones, 4) def test_nbinstall(self): temp_dir = gettempdir() target_path = join(temp_dir, 'share/jupyter/nbextensions/emperor/' 'support_files') # remove the whole tree self.files_to_delete.append(join(temp_dir, 'share')) nbinstall(prefix=temp_dir, user=None) self.assertTrue(exists(target_path)) def test_custom_axes(self): columns = ['SampleID', 'BarcodeSequence', 'LinkerPrimerSequence', 'Treatment', 'DOB', 'Description'] mf = pd.DataFrame(data=MAPPING_FILE_DATA, columns=columns) obs = validate_and_process_custom_axes(mf, ['DOB']) exp = pd.DataFrame(data=MAPPING_FILE_DATA_CONVERTED, columns=columns) pd.util.testing.assert_frame_equal(obs, exp) def test_custom_axes_non_existent_names(self): columns = ['SampleID', 'BarcodeSequence', 'LinkerPrimerSequence', 'Treatment', 'DOB', 'Description'] mf = pd.DataFrame(data=MAPPING_FILE_DATA, columns=columns) with self.assertRaises(KeyError): validate_and_process_custom_axes(mf, [':L']) with self.assertRaises(KeyError): validate_and_process_custom_axes(mf, ['D0B']) def test_custom_axes_non_numeric_values(self): columns = ['SampleID', 'BarcodeSequence', 'LinkerPrimerSequence', 'Treatment', 'DOB', 'Description'] mf = pd.DataFrame(data=MAPPING_FILE_DATA, columns=columns) with self.assertRaises(ValueError): validate_and_process_custom_axes(mf, ['Treatment']) with self.assertRaises(ValueError): validate_and_process_custom_axes(mf, ['SampleID']) def test_custom_axes_non_numeric_values_mixed(self): columns = ['SampleID', 'huey', 'dewey', 'louie', 'Description'] mf = pd.DataFrame(data=BROKEN_MAPPING_FILE, columns=columns) with self.assertRaises(ValueError): validate_and_process_custom_axes(mf, ['louie']) with self.assertRaises(ValueError): validate_and_process_custom_axes(mf, ['louie', 'dewey']) def test_resolve_stable_url_release(self): # we test that no warnings are raised url = 'https://github.com/biocore/emperor/%s/emperor/support_files' with warnings.catch_warnings(record=True) as w: obs = resolve_stable_url('1.0.0b7', url) self.assertTrue(len(w) == 0) self.assertEqual(obs, url % '1.0.0-beta.7') def test_resolve_stable_url_release_check_warning(self): url = 'https://github.com/biocore/emperor/%s/emperor/support_files' with warnings.catch_warnings(record=True) as w: warnings.simplefilter('always') obs = resolve_stable_url('1.0.0b7-dev', url) self.assertTrue(len(w) == 1) self.assertTrue(issubclass(w[-1].category, EmperorWarning)) self.assertEqual(obs, url % 'new-api') def test_resolve_stable_url_release_number_check_warning(self): url = 'https://github.com/biocore/emperor/%s/emperor/support_files' with warnings.catch_warnings(record=True) as w: warnings.simplefilter('always') obs = resolve_stable_url('1.0.0b7-dev0', url) self.assertTrue(len(w) == 1) self.assertTrue(issubclass(w[-1].category, EmperorWarning)) self.assertEqual(obs, url % 'new-api') MAPPING_FILE_DATA = [ ['PC.354', 'AGCACGAGCCTA', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061218', 'Control_mouse_I.D._354'], ['PC.355', 'AACTCGTCGATG', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061218', 'Control_mouse_I.D._355'], ['PC.356', 'ACAGACCACTCA', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061126', 'Control_mouse_I.D._356'], ['PC.481', 'ACCAGCGACTAG', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20070314', 'Control_mouse_I.D._481'], ['PC.593', 'AGCAGCACTTGT', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20071210', 'Control_mouse_I.D._593'], ['PC.607', 'AACTGTGCGTAC', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20071112', 'Fasting_mouse_I.D._607'], ['PC.634', 'ACAGAGTCGGCT', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116', 'Fasting_mouse_I.D._634'], ['PC.635', 'ACCGCAGAGTCA', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116', 'Fasting_mouse_I.D._635'], ['PC.636', 'ACGGTGAGTGTC', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116', 'Fasting_mouse_I.D._636']] MAPPING_FILE_DATA_CONVERTED = [ ['PC.354', 'AGCACGAGCCTA', 'YATGCTGCCTCCCGTAGGAGT', 'Control', 20061218, 'Control_mouse_I.D._354'], ['PC.355', 'AACTCGTCGATG', 'YATGCTGCCTCCCGTAGGAGT', 'Control', 20061218, 'Control_mouse_I.D._355'], ['PC.356', 'ACAGACCACTCA', 'YATGCTGCCTCCCGTAGGAGT', 'Control', 20061126, 'Control_mouse_I.D._356'], ['PC.481', 'ACCAGCGACTAG', 'YATGCTGCCTCCCGTAGGAGT', 'Control', 20070314, 'Control_mouse_I.D._481'], ['PC.593', 'AGCAGCACTTGT', 'YATGCTGCCTCCCGTAGGAGT', 'Control', 20071210, 'Control_mouse_I.D._593'], ['PC.607', 'AACTGTGCGTAC', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', 20071112, 'Fasting_mouse_I.D._607'], ['PC.634', 'ACAGAGTCGGCT', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', 20080116, 'Fasting_mouse_I.D._634'], ['PC.635', 'ACCGCAGAGTCA', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', 20080116, 'Fasting_mouse_I.D._635'], ['PC.636', 'ACGGTGAGTGTC', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', 20080116, 'Fasting_mouse_I.D._636']] PRE_PROCESS_A = [ ['PC.354', 'AGCACGAGCCTA', 'Control', '20061218'], ['PC.355', 'AACTCGTCGATG', 'Control', '20061218'], ['PC.356', 'ACAGACCACTCA', 'Control', '20061126'], ['PC.481', 'ACCAGCGACTAG', 'Control', '20070314'], ['PC.593', 'AGCAGCACTTGT', 'Control', '20071210'], ['PC.607', 'AACTGTGCGTAC', 'Fast', '20071112'], ['PC.634', 'ACAGAGTCGGCT', 'Fast', '20080116'], ['PC.635', 'ACCGCAGAGTCA', 'Fast', '20080116'], ['PC.636', 'ACGGTGAGTGTC', 'Fast', '20080116']] PRE_PROCESS_B = [ ['PC.354', 'YATGCTGCCTCCCGTAGGAGT', 'Control_mouse_I.D._354'], ['PC.355', 'YATGCTGCCTCCCGTAGGAGT', 'Control_mouse_I.D._355'], ['PC.356', 'YATGCTGCCTCCCGTAGGAGT', 'Control_mouse_I.D._356'], ['PC.481', 'YATGCTGCCTCCCGTAGGAGT', 'Control_mouse_I.D._481'], ['PC.593', 'YATGCTGCCTCCCGTAGGAGT', 'Control_mouse_I.D._593'], ['PC.607', 'YATGCTGCCTCCCGTAGGAGT', 'Fasting_mouse_I.D._607'], ['PC.634', 'YATGCTGCCTCCCGTAGGAGT', 'Fasting_mouse_I.D._634'], ['PC.635', 'YATGCTGCCTCCCGTAGGAGT', 'Fasting_mouse_I.D._635'], ['PC.636', 'YATGCTGCCTCCCGTAGGAGT', 'Fasting_mouse_I.D._636']] MAPPING_FILE_DATA_CAT_A = [ ['PC.354', 'Control', '20061218', 'Control20061218'], ['PC.355', 'Control', '20061218', 'Control20061218'], ['PC.356', 'Control', '20061126', 'Control20061126'], ['PC.481', 'Control', '20070314', 'Control20070314'], ['PC.593', 'Control', '20071210', 'Control20071210'], ['PC.607', 'Fast', '20071112', 'Fast20071112'], ['PC.634', 'Fast', '20080116', 'Fast20080116'], ['PC.635', 'Fast', '20080116', 'Fast20080116'], ['PC.636', 'Fast', '20080116', 'Fast20080116']] MAPPING_FILE_DATA_CAT_B = [ ['PC.354', 'Control', '20061218', '20061218Control'], ['PC.355', 'Control', '20061218', '20061218Control'], ['PC.356', 'Control', '20061126', '20061126Control'], ['PC.481', 'Control', '20070314', '20070314Control'], ['PC.593', 'Control', '20071210', '20071210Control'], ['PC.607', 'Fast', '20071112', '20071112Fast'], ['PC.634', 'Fast', '20080116', '20080116Fast'], ['PC.635', 'Fast', '20080116', '20080116Fast'], ['PC.636', 'Fast', '20080116', '20080116Fast']] MAPPING_FILE_DATA_CAT_C = [ ['PC.354', 'Control'], ['PC.355', 'Control'], ['PC.356', 'Control'], ['PC.481', 'Control'], ['PC.593', 'Control'], ['PC.607', 'Fast'], ['PC.634', 'Fast'], ['PC.635', 'Fast'], ['PC.636', 'Fast']] MAPPING_FILE_DATA_CAT_D = [ ['PC.354', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061218'], ['PC.355', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061218'], ['PC.356', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061126'], ['PC.481', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20070314'], ['PC.593', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20071210'], ['PC.607', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20071112'], ['PC.634', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116'], ['PC.635', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116'], ['PC.636', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116']] MAPPING_FILE_DATA_CAT_E = [ ['PC.354', 'AGCACGAGCCTA', 'Control', '20061218', 'Control_mouse_I.D._354'], ['PC.355', 'AACTCGTCGATG', 'Control', '20061218', 'Control_mouse_I.D._355'], ['PC.356', 'ACAGACCACTCA', 'Control', '20061126', 'Control_mouse_I.D._356'], ['PC.481', 'ACCAGCGACTAG', 'Control', '20070314', 'Control_mouse_I.D._481'], ['PC.593', 'AGCAGCACTTGT', 'Control', '20071210', 'Control_mouse_I.D._593'], ['PC.607', 'AACTGTGCGTAC', 'Fast', '20071112', 'Fasting_mouse_I.D._607'], ['PC.634', 'ACAGAGTCGGCT', 'Fast', '20080116', 'Fasting_mouse_I.D._634'], ['PC.635', 'ACCGCAGAGTCA', 'Fast', '20080116', 'Fasting_mouse_I.D._635'], ['PC.636', 'ACGGTGAGTGTC', 'Fast', '20080116', 'Fasting_mouse_I.D._636']] MAPPING_FILE_DATA_CAT_F = [ ['PC.354', 'Control', 'Control20061218'], ['PC.355', 'Control', 'Control20061218'], ['PC.356', 'Control', 'Control20061126'], ['PC.481', 'Control', 'Control20070314'], ['PC.593', 'Control', 'Control20071210'], ['PC.607', 'Fast', 'Fast20071112'], ['PC.634', 'Fast', 'Fast20080116'], ['PC.635', 'Fast', 'Fast20080116'], ['PC.636', 'Fast', 'Fast20080116']] MAPPING_FILE_DATA_CAT_G = [ ['PC.354', 'AGCACGAGCCTA', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061218', 'Control_mouse_I.D._354'], ['PC.355', 'AACTCGTCGATG', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061218', 'Control_mouse_I.D._355'], ['PC.356', 'ACAGACCACTCA', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061126', 'Control_mouse_I.D._356'], ['PC.481', 'ACCAGCGACTAG', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20070314', 'Control_mouse_I.D._481'], ['PC.593', 'AGCAGCACTTGT', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20071210', 'Control_mouse_I.D._593'], ['PC.607', 'AACTGTGCGTAC', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20071112', 'Fasting_mouse_I.D._607'], ['PC.634', 'ACAGAGTCGGCT', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116', 'Fasting_mouse_I.D._634'], ['PC.635', 'ACCGCAGAGTCA', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116', 'Fasting_mouse_I.D._635'], ['PC.636', 'ACGGTGAGTGTC', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116', 'Fasting_mouse_I.D._636']] MAPPING_FILE_DATA_CAT_H = [ ['PC.354', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061218'], ['PC.355', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061218'], ['PC.356', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20061126'], ['PC.481', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20070314'], ['PC.593', 'YATGCTGCCTCCCGTAGGAGT', 'Control', '20071210'], ['PC.607', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20071112'], ['PC.634', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116'], ['PC.635', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116'], ['PC.636', 'YATGCTGCCTCCCGTAGGAGT', 'Fast', '20080116']] MAPPING_FILE_DATA_GRADIENT = [ ['PC.354', 'Control', '3', '40', 'Control20061218'], ['PC.355', 'Control', '9', '44', 'Control20061218'], ['PC.635', 'Fast', '9', '44', 'Fast20080116'], ['PC.636', 'Fast', '12', '37.22', 'Fast20080116']] MAPPING_FILE_DATA_DUPLICATED = [ ['PC.354_0', 'Control', '20061218'], ['PC.355_0', 'Control', '20061218'], ['PC.356_0', 'Control', '20061126'], ['PC.481_0', 'Control', '20070314'], ['PC.593_0', 'Control', '20071210'], ['PC.607_0', 'Fast', '20071112'], ['PC.634_0', 'Fast', '20080116'], ['PC.635_0', 'Fast', '20080116'], ['PC.636_0', 'Fast', '20080116'], ['PC.354_1', 'Control', '20061218'], ['PC.355_1', 'Control', '20061218'], ['PC.356_1', 'Control', '20061126'], ['PC.481_1', 'Control', '20070314'], ['PC.593_1', 'Control', '20071210'], ['PC.607_1', 'Fast', '20071112'], ['PC.634_1', 'Fast', '20080116'], ['PC.635_1', 'Fast', '20080116'], ['PC.636_1', 'Fast', '20080116'], ['PC.354_2', 'Control', '20061218'], ['PC.355_2', 'Control', '20061218'], ['PC.356_2', 'Control', '20061126'], ['PC.481_2', 'Control', '20070314'], ['PC.593_2', 'Control', '20071210'], ['PC.607_2', 'Fast', '20071112'], ['PC.634_2', 'Fast', '20080116'], ['PC.635_2', 'Fast', '20080116'], ['PC.636_2', 'Fast', '20080116']] COORDS_DATA = array([ [-0.2, -0.1, 0.06, -0.06], [-0.3, 0.04, -0.1, 0.15], [0.1, -0.1, -0.2, 0.08], [0.04, -0.01, 0.06, -0.34]]) BROKEN_MAPPING_FILE = [ ['PC.354', 'Control', '3', '40', 'Control20061218'], ['PC.355', 'Control', 'y', '44', 'Control20061218'], ['PC.635', 'Fast', '9', 'x', 'Fast20080116'], ['PC.636', 'Fast', '12', '37.22', 'Fast20080116']] BROKEN_MAPPING_FILE_2_VALUES = [ ['PC.354', 'Control', '3', '40', 'Control20061218'], ['PC.355', 'Control', 'NA', '44', 'Control20061218'], ['PC.635', 'Fast', 'NA', 'x', 'Fast20080116'], ['PC.636', 'Fast', '12', '37.22', 'Fast20080116']] UNSANITZIED_MAPPING_DATA = [ ['PC.354', "Dr. Bronner's", 'Cont"rol', '20061218', 'Control_mouse_I.D._354'], ['PC.355', 'AACTCGTCGATG', "Con''trol", '20061218', 'Control_mouse_I.D._355'], ["PC'356", 'ACAGACCACTCA', 'Control', '20061126', 'Control_mouse_I.D._"356'], ['PC.481', 'AC"AGC"ACTAG', 'Control', '20070314', 'Control_mouse_I.D._481'], ['PC.593', 'AGCAGCACTTGT', 'Control', '20071210', 'Control_mouse_I.D._593']] if __name__ == "__main__": main()