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# ----------------------------------------------------------------------------
# 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 <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()
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