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