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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 COPYING.txt, distributed with this software.
# ----------------------------------------------------------------------------
import unittest
import pandas as pd
import numpy as np
from skbio.util import get_data_path, assert_data_frame_almost_equal
from skbio.io.format.blast6 import _blast6_to_data_frame
class TestBlast6Reader(unittest.TestCase):
def test_default_valid_single_line(self):
fp = get_data_path('blast6_default_single_line')
df = _blast6_to_data_frame(fp, default_columns=True)
exp = pd.DataFrame([['query1', 'subject2', 75.0, 8.0, 2.0, 0.0, 1.0,
8.0, 2.0, 9.0, 0.06, 11.5]],
columns=['qseqid', 'sseqid', 'pident', 'length',
'mismatch', 'gapopen', 'qstart', 'qend',
'sstart', 'send', 'evalue', 'bitscore'])
assert_data_frame_almost_equal(df, exp)
def test_default_valid_multi_line(self):
fp = get_data_path('blast6_default_multi_line')
df = _blast6_to_data_frame(fp, default_columns=True)
exp = pd.DataFrame([['query1', 'subject2', 100.00, 8.0, 0.0, 0.0, 1.0,
8.0, 3.0, 10.0, 9e-05, 16.9],
['query1', 'subject2', 75.00, 8.0, 2.0, 0.0, 1.0,
8.0, 2.0, 9.0, 0.060, 11.5],
['query2', 'subject1', 71.43, 7.0, 2.0, 0.0, 1.0,
7.0, 1.0, 7.0, 0.044, 11.9]],
columns=['qseqid', 'sseqid', 'pident', 'length',
'mismatch', 'gapopen', 'qstart', 'qend',
'sstart', 'send', 'evalue', 'bitscore'])
assert_data_frame_almost_equal(df, exp)
def test_custom_valid_single_line(self):
fp = get_data_path('blast6_custom_single_line')
df = _blast6_to_data_frame(fp, columns=['qacc', 'qseq', 'btop',
'sframe', 'ppos',
'positive', 'gaps'])
exp = pd.DataFrame([['query1', 'PAAWWWWW', 8.0, 1.0, 100.00, 8.0,
0.0]], columns=['qacc', 'qseq', 'btop', 'sframe',
'ppos', 'positive', 'gaps'])
assert_data_frame_almost_equal(df, exp)
def test_custom_valid_multi_line(self):
fp = get_data_path('blast6_custom_multi_line')
df = _blast6_to_data_frame(fp, columns=['sacc', 'score', 'gapopen',
'qcovs', 'sblastnames',
'sallacc', 'qaccver'])
exp = pd.DataFrame([['subject2', 32.0, 0.0, 100.0, np.nan, 'subject2',
'query1'], ['subject2', 18.0, 0.0, 100.0, np.nan,
'subject2', 'query1'],
['subject1', 19.0, 0.0, 70.0, np.nan, 'subject1',
'query2']], columns=['sacc', 'score', 'gapopen',
'qcovs', 'sblastnames',
'sallacc', 'qaccver'])
exp['sblastnames'] = exp['sblastnames'].astype(object)
assert_data_frame_almost_equal(df, exp)
def test_valid_nan_handling(self):
fp = get_data_path('blast6_custom_mixed_nans')
df = _blast6_to_data_frame(fp, columns=['qacc', 'qseq', 'btop',
'sframe', 'ppos', 'positive',
'gaps'])
exp = pd.DataFrame([[np.nan, 'PAAWWWWW', 8.0, 1.0, 100.00, np.nan,
0.0], ['query1', np.nan, 8.0, 1.0, np.nan, 8.0,
0.0]], columns=['qacc', 'qseq', 'btop',
'sframe', 'ppos',
'positive', 'gaps'])
assert_data_frame_almost_equal(df, exp)
def test_valid_minimal(self):
fp = get_data_path('blast6_custom_minimal')
df = _blast6_to_data_frame(fp, columns=['sacc'])
exp = pd.DataFrame([['subject2']], columns=['sacc'])
assert_data_frame_almost_equal(df, exp)
def test_custom_and_default_passed_error(self):
fp = get_data_path('blast6_default_single_line')
with self.assertRaisesRegex(ValueError,
"`columns` and `default_columns`"):
_blast6_to_data_frame(fp, columns=['qseqid'], default_columns=True)
def test_no_columns_passed_error(self):
fp = get_data_path('blast6_default_single_line')
with self.assertRaisesRegex(ValueError,
"Either `columns` or `default_columns`"):
_blast6_to_data_frame(fp)
def test_wrong_amount_of_columns_error(self):
fp = get_data_path('blast6_invalid_number_of_columns')
with self.assertRaisesRegex(
ValueError, "Specified number of columns \(12\).*\(10\)"):
_blast6_to_data_frame(fp, default_columns=True)
def test_different_data_in_same_column(self):
fp = get_data_path('blast6_invalid_type_in_column')
with self.assertRaises(ValueError):
_blast6_to_data_frame(fp, default_columns=True)
def test_wrong_column_name_error(self):
fp = get_data_path('blast6_default_single_line')
with self.assertRaisesRegex(ValueError,
"Unrecognized column.*'abcd'"):
_blast6_to_data_frame(fp, columns=['qseqid', 'sseqid', 'pident',
'length', 'mismatch', 'gapopen',
'qstart', 'qend', 'sstart',
'send', 'abcd', 'bitscore'])
if __name__ == '__main__':
unittest.main()
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