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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 import BLAST7FormatError
from skbio.io.format.blast7 import _blast7_to_data_frame, _blast7_sniffer
class TestBLAST7Sniffer(unittest.TestCase):
def setUp(self):
self.positives = [get_data_path(e) for e in [
'blast7_default_single_line',
'blast7_default_multi_line',
'blast7_custom_minimal',
'blast7_custom_single_line',
'blast7_custom_multi_line',
'blast7_custom_mixed_nans',
'blast7_invalid_differing_fields',
'blast7_invalid_no_data',
'blast7_invalid_too_many_columns',
'legacy9_and_blast7_default',
'legacy9_invalid_too_many_columns',
'legacy9_mixed_nans',
'legacy9_multi_line',
'legacy9_single_line']]
self.negatives = [get_data_path(e) for e in [
'blast7_invalid_gibberish',
'blast7_invalid_for_sniffer',
'blast7_invalid_for_sniffer_2',
'empty']]
def test_positives(self):
for fp in self.positives:
self.assertEqual(_blast7_sniffer(fp), (True, {}))
def test_negatives(self):
for fp in self.negatives:
self.assertEqual(_blast7_sniffer(fp), (False, {}))
class TestBlast7Reader(unittest.TestCase):
def test_default_valid_single_line(self):
fp = get_data_path('blast7_default_single_line')
df = _blast7_to_data_frame(fp)
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]],
columns=['qseqid', 'sseqid', 'pident', 'length',
'mismatch', 'gapopen', 'qstart', 'qend',
'sstart', 'send', 'evalue', 'bitscore'])
assert_data_frame_almost_equal(df, exp)
fp = get_data_path('legacy9_single_line')
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([['query1', 'subject1', 90.00, 7.0, 1.0, 0.0, 0.0,
8.0, 4.0, 10.0, 1e-05, 15.5]],
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('blast7_default_multi_line')
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([['query1', 'subject2', 70.00, 5.0, 0.0, 0.0, 7.0,
60.0, 3.0, 100.0, 9e-05, 10.5],
['query1', 'subject2', 30.00, 8.0, 0.0, 0.0, 6.0,
15.0, 1.0, 100.0, 0.053, 12.0],
['query1', 'subject2', 90.00, 2.0, 0.0, 0.0, 9.0,
35.0, 2.0, 100.0, 0.002, 8.3]],
columns=['qseqid', 'sseqid', 'pident', 'length',
'mismatch', 'gapopen', 'qstart', 'qend',
'sstart', 'send', 'evalue', 'bitscore'])
assert_data_frame_almost_equal(df, exp)
fp = get_data_path('legacy9_multi_line')
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([['query1', 'subject1', 90.00, 7.0, 1.0, 0.0, 0.0,
8.0, 4.0, 10.0, 1e-05, 15.5],
['query1', 'subject1', 70.00, 8.0, 0.0, 1.0, 0.0,
9.0, 5.0, 7.0, 0.231, 7.8],
['query1', 'subject1', 90.00, 5.0, 1.0, 1.0, 0.0,
0.0, 2.0, 10.0, 0.022, 13.0]],
columns=['qseqid', 'sseqid', 'pident', 'length',
'mismatch', 'gapopen', 'qstart', 'qend',
'sstart', 'send', 'evalue', 'bitscore'])
assert_data_frame_almost_equal(df, exp)
def test_default_valid_mixed_output(self):
fp = get_data_path('legacy9_and_blast7_default')
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([['query2', 'subject2', 100.00, 8.0, 0.0, 1.0, 0.0,
9.0, 3.0, 10.0, 2e-05, 9.8],
['query2', 'subject1', 70.00, 9.0, 1.0, 0.0, 1.0,
8.0, 4.0, 9.0, 0.025, 11.7]],
columns=['qseqid', 'sseqid', 'pident', 'length',
'mismatch', 'gapopen', 'qstart', 'qend',
'sstart', 'send', 'evalue', 'bitscore'])
assert_data_frame_almost_equal(df, exp)
def test_custom_valid_minimal(self):
fp = get_data_path("blast7_custom_minimal")
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([['query1']], columns=['qseqid'])
assert_data_frame_almost_equal(df, exp)
def test_custom_valid_single_line(self):
fp = get_data_path("blast7_custom_single_line")
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([['query1', 100.00, 100.00, 8.0, 0.0, 16.9, 8.0,
'PAAWWWWW']],
columns=['qseqid', 'ppos', 'pident', 'length',
'sgi', 'bitscore', 'qend', 'qseq'])
assert_data_frame_almost_equal(df, exp)
def test_custom_valid_multi_line(self):
fp = get_data_path("blast7_custom_multi_line")
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([[1.0, 8.0, 3.0, 10.0, 8.0, 0.0, 1.0, 'query1',
'subject2'],
[2.0, 5.0, 2.0, 15.0, 8.0, 0.0, 2.0, 'query1',
'subject2'],
[1.0, 6.0, 2.0, 12.0, 8.0, 0.0, 1.0, 'query1',
'subject2']],
columns=['qstart', 'qend', 'sstart', 'send',
'nident', 'mismatch', 'sframe',
'qaccver', 'saccver'])
assert_data_frame_almost_equal(df, exp)
def test_custom_valid_mixed_nans(self):
fp = get_data_path("blast7_custom_mixed_nans")
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([[0.0, np.nan, 8.0, 13.0, 1.0, 1.0, np.nan,
'subject2'],
[np.nan, 0.0, 8.0, np.nan, 1.0, 1.0, 'query1',
np.nan]],
columns=['qgi', 'sgi', 'qlen', 'slen', 'qframe',
'sframe', 'qseqid', 'sseqid'])
assert_data_frame_almost_equal(df, exp)
def test_legacy9_valid_mixed_nans(self):
fp = get_data_path("legacy9_mixed_nans")
df = _blast7_to_data_frame(fp)
exp = pd.DataFrame([[np.nan, 'subject1', np.nan, 7.0, 1.0, 0.0, np.nan,
8.0, 4.0, 10.0, np.nan, 15.5],
['query2', 'subject1', 90.00, 8.0, np.nan, 0.0,
0.0, 8.0, np.nan, 9.0, 1e-05, np.nan]],
columns=['qseqid', 'sseqid', 'pident', 'length',
'mismatch', 'gapopen', 'qstart', 'qend',
'sstart', 'send', 'evalue', 'bitscore'])
assert_data_frame_almost_equal(df, exp)
def test_differing_fields_error(self):
fp = get_data_path("blast7_invalid_differing_fields")
with self.assertRaisesRegex(
BLAST7FormatError,
"Fields \[.*'qseqid', .*'sseqid', .*'qstart'\]"
" do.*\[.*'qseqid', .*'sseqid', .*'score'\]"):
_blast7_to_data_frame(fp)
fp = get_data_path("legacy9_invalid_differing_fields")
with self.assertRaisesRegex(
BLAST7FormatError,
"Fields \[.*'qseqid', .*'sseqid', .*'qstart'\]"
" do.*\[.*'qseqid', .*'sseqid', "
".*'sallseqid'\]"):
_blast7_to_data_frame(fp)
def test_no_data_error(self):
fp = get_data_path("blast7_invalid_gibberish")
with self.assertRaisesRegex(BLAST7FormatError,
"File contains no"):
_blast7_to_data_frame(fp)
fp = get_data_path("blast7_invalid_no_data")
with self.assertRaisesRegex(BLAST7FormatError,
"File contains no"):
_blast7_to_data_frame(fp)
fp = get_data_path("empty")
with self.assertRaisesRegex(BLAST7FormatError,
"File contains no"):
_blast7_to_data_frame(fp)
def test_wrong_amount_of_columns_error(self):
fp = get_data_path("blast7_invalid_too_many_columns")
with self.assertRaisesRegex(BLAST7FormatError,
"Number of fields.*\(2\)"):
_blast7_to_data_frame(fp)
fp = get_data_path("legacy9_invalid_too_many_columns")
with self.assertRaisesRegex(BLAST7FormatError,
"Number of fields.*\(12\)"):
_blast7_to_data_frame(fp)
def test_unrecognized_field_error(self):
fp = get_data_path("blast7_invalid_unrecognized_field")
with self.assertRaisesRegex(BLAST7FormatError,
"Unrecognized field \(.*'sallid'\)"):
_blast7_to_data_frame(fp)
if __name__ == '__main__':
unittest.main()
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