# ---------------------------------------------------------------------------- # Copyright (c) 2013--, scikit-bio development team. # # Distributed under the terms of the Modified BSD License. # # The full license is in the file LICENSE.txt, distributed with this software. # ---------------------------------------------------------------------------- import unittest from io import StringIO import pandas as pd import numpy as np from skbio.util import get_data_path, assert_data_frame_almost_equal from skbio.io.format.taxdump import _taxdump_to_data_frame class TestTaxdumpReader(unittest.TestCase): def test_nodes_default(self): # subset of a real NCBI taxonomy nodes.dmp file fp = get_data_path('taxdump_nodes.dmp') obs = _taxdump_to_data_frame(fp, scheme='nodes') exp = pd.DataFrame([ [1, 1, 'no rank', np.nan, 8, False, 1, False, 0, False, False, False, np.nan], [2, 131567, 'superkingdom', np.nan, 0, False, 11, False, 0, False, False, False, np.nan], [543, 91347, 'family', np.nan, 0, True, 11, True, 0, True, False, False, np.nan], [548, 570, 'species', 'KA', 0, True, 11, True, 0, True, True, False, np.nan], [561, 543, 'genus', np.nan, 0, True, 11, True, 0, True, False, False, np.nan], [562, 561, 'species', 'EC', 0, True, 11, True, 0, True, True, False, np.nan], [570, 543, 'genus', np.nan, 0, True, 11, True, 0, True, False, False, np.nan], [620, 543, 'genus', np.nan, 0, True, 11, True, 0, True, False, False, np.nan], [622, 620, 'species', 'SD', 0, True, 11, True, 0, True, True, False, np.nan], [766, 28211, 'order', np.nan, 0, True, 11, True, 0, True, False, False, np.nan], [1224, 2, 'phylum', np.nan, 0, True, 11, True, 0, True, False, False, np.nan], [1236, 1224, 'class', np.nan, 0, True, 11, True, 0, True, False, False, np.nan], [28211, 1224, 'class', np.nan, 0, True, 11, True, 0, True, False, False, np.nan], [91347, 1236, 'order', np.nan, 0, True, 11, True, 0, True, False, False, np.nan], [118884, 1236, 'no rank', np.nan, 0, True, 11, True, 0, True, True, False, np.nan], [126792, 36549, 'species', 'PP', 0, True, 11, True, 0, True, True, False, np.nan], [131567, 1, 'no rank', np.nan, 8, True, 1, True, 0, True, True, False, np.nan], [585056, 562, 'no rank', np.nan, 0, True, 11, True, 0, True, True, False, np.nan], [1038927, 562, 'no rank', np.nan, 0, True, 11, True, 0, True, True, False, np.nan], [2580236, 488338, 'species', 'SE', 7, True, 11, True, 0, True, False, False, np.nan]], columns=[ 'tax_id', 'parent_tax_id', 'rank', 'embl_code', 'division_id', 'inherited_div_flag', 'genetic_code_id', 'inherited_GC_flag', 'mitochondrial_genetic_code_id', 'inherited_MGC_flag', 'GenBank_hidden_flag', 'hidden_subtree_root_flag', 'comments']).set_index('tax_id') exp['comments'] = exp['comments'].astype('O') assert_data_frame_almost_equal(obs, exp) def test_names_default(self): # subset of a real NCBI taxonomy names.dmp file fp = get_data_path('taxdump_names.dmp') obs = _taxdump_to_data_frame(fp, scheme='names') exp = pd.DataFrame([ [1, 'root', np.nan, 'scientific name'], [2, 'Bacteria', 'Bacteria ', 'scientific name'], [2, 'eubacteria', np.nan, 'genbank common name'], [543, 'Enterobacteriaceae', np.nan, 'scientific name'], [548, 'Klebsiella aerogenes', np.nan, 'scientific name'], [561, 'Escherichia', np.nan, 'scientific name'], [562, '"Bacillus coli" Migula 1895', np.nan, 'authority'], [562, 'Escherichia coli', np.nan, 'scientific name'], [562, 'Escherichia/Shigella coli', np.nan, 'equivalent name'], [570, 'Donovania', np.nan, 'synonym'], [570, 'Klebsiella', np.nan, 'scientific name'], [620, 'Shigella', np.nan, 'scientific name'], [622, 'Shigella dysenteriae', np.nan, 'scientific name'], [766, 'Rickettsiales', np.nan, 'scientific name'], [1224, 'Proteobacteria', np.nan, 'scientific name'], [1236, 'Gammaproteobacteria', np.nan, 'scientific name'], [28211, 'Alphaproteobacteria', np.nan, 'scientific name'], [91347, 'Enterobacterales', np.nan, 'scientific name'], [118884, 'unclassified Gammaproteobacteria', np.nan, 'scientific name'], [126792, 'Plasmid pPY113', np.nan, 'scientific name'], [131567, 'cellular organisms', np.nan, 'scientific name'], [585056, 'Escherichia coli UMN026', np.nan, 'scientific name'], [1038927, 'Escherichia coli O104:H4', np.nan, 'scientific name'], [2580236, 'synthetic Escherichia coli Syn61', np.nan, 'scientific name']], columns=['tax_id', 'name_txt', 'unique_name', 'name_class']).set_index('tax_id') assert_data_frame_almost_equal(obs, exp) def test_nodes_slim(self): fp = get_data_path('taxdump_nodes.dmp') obs = _taxdump_to_data_frame(fp, scheme='nodes_slim') exp = pd.DataFrame([ [1, 1, 'no rank'], [2, 131567, 'superkingdom'], [543, 91347, 'family'], [548, 570, 'species'], [561, 543, 'genus'], [562, 561, 'species'], [570, 543, 'genus'], [620, 543, 'genus'], [622, 620, 'species'], [766, 28211, 'order'], [1224, 2, 'phylum'], [1236, 1224, 'class'], [28211, 1224, 'class'], [91347, 1236, 'order'], [118884, 1236, 'no rank'], [126792, 36549, 'species'], [131567, 1, 'no rank'], [585056, 562, 'no rank'], [1038927, 562, 'no rank'], [2580236, 488338, 'species']], columns=['tax_id', 'parent_tax_id', 'rank']).set_index('tax_id') assert_data_frame_almost_equal(obs, exp) def test_custom_scheme(self): fs = StringIO('\n'.join(map('\t|\t'.join, [ ('a', 'a'), ('b', 'a'), ('c', 'a') ]))) obs = _taxdump_to_data_frame(fs, scheme={'self': str, 'parent': str}) exp = pd.DataFrame([ ['a', 'a'], ['b', 'a'], ['c', 'a']], columns=['self', 'parent']).set_index('self') assert_data_frame_almost_equal(obs, exp) def test_invalid_scheme(self): fp = get_data_path('taxdump_names.dmp') with self.assertRaises(ValueError) as ctx: _taxdump_to_data_frame(fp, scheme='hello') self.assertEqual(str(ctx.exception), 'Invalid taxdump column scheme: "hello".') def test_invalid_id(self): fs = StringIO('\n'.join(map('\t|\t'.join, [ ('1', '2', 'family'), ('3', '4', 'genus'), ('x', '6', 'species'), # 'x' is not a number ]))) with self.assertRaises(ValueError) as ctx: _taxdump_to_data_frame(fs, scheme='nodes_slim') self.assertEqual(str(ctx.exception), 'Invalid taxdump file format.') if __name__ == '__main__': unittest.main()