# ---------------------------------------------------------------------------- # 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 io import unittest from skbio.io import PhylipFormatError from skbio.io.format.phylip import ( _tabular_msa_to_phylip, _phylip_to_tabular_msa, _phylip_sniffer) from skbio import TabularMSA, DNA, RNA from skbio.util import get_data_path class TestSniffer(unittest.TestCase): def setUp(self): self.positives = [get_data_path(e) for e in [ 'phylip_dna_3_seqs', 'phylip_single_seq_long', 'phylip_single_seq_short', 'phylip_two_chunks', 'phylip_variable_length_ids', 'phylip_varied_whitespace_in_seqs', 'phylip_whitespace_in_header_1', 'phylip_whitespace_in_header_2', 'phylip_whitespace_in_header_3', ]] # negative tests for sniffer don't include # phylip_invalid_empty_line_between_seqs, phylip_invalid_too_few_seqs, # phylip_invalid_too_many_seqs - because sniffer only reads first seq self.negatives = [get_data_path(e) for e in [ 'empty', 'whitespace_only', 'phylip_invalid_empty_line_after_header', 'phylip_invalid_empty_line_before_header', 'phylip_invalid_header_too_long', 'phylip_invalid_header_too_short', 'phylip_invalid_no_header', 'phylip_invalid_seq_too_long', 'phylip_invalid_seq_too_short', 'phylip_invalid_zero_seq_len', 'phylip_invalid_zero_seqs', ]] def test_positives(self): for fp in self.positives: self.assertEqual(_phylip_sniffer(fp), (True, {})) def test_negatives(self): for fp in self.negatives: self.assertEqual(_phylip_sniffer(fp), (False, {})) class TestReaders(unittest.TestCase): def setUp(self): self.valid_configurations = [ ([get_data_path('phylip_dna_3_seqs')], [('..ACC-GTTGG..', 'd1'), ('TTACCGGT-GGCC', 'd2'), ('.-ACC-GTTGC--', 'd3')] ), ([get_data_path('phylip_single_seq_long')], [('..ACC-GTTGG..AATGC.C----', 'foo')] ), ([get_data_path('phylip_single_seq_short')], [('-', '')] ), ([get_data_path('phylip_two_chunks'), get_data_path('phylip_varied_whitespace_in_seqs'), get_data_path('phylip_whitespace_in_header_1'), get_data_path('phylip_whitespace_in_header_2'), get_data_path('phylip_whitespace_in_header_3'), ], [('..ACC-GTTGG..AATGC.C', 'foo'), ('TTACCGGT-GGCCTA-GCAT', 'bar')] ), ([get_data_path('phylip_variable_length_ids')], [('.-ACGT', ''), ('TGCA-.', 'a'), ('.ACGT-', 'bb'), ('TGCA-.', '1'), ('AAAAAA', 'abcdefghij'), ('GGGGGG', 'ab def42ij')] ), ] self.positive_fps = list(map(get_data_path, [ 'phylip_dna_3_seqs', 'phylip_single_seq_long', 'phylip_single_seq_short', 'phylip_two_chunks', 'phylip_variable_length_ids', 'phylip_varied_whitespace_in_seqs', 'phylip_whitespace_in_header_1', 'phylip_whitespace_in_header_2', 'phylip_whitespace_in_header_3', ])) self.invalid_files = [(get_data_path(e[0]), e[1], e[2]) for e in [ ('empty', PhylipFormatError, 'This file is empty.'), ('whitespace_only', PhylipFormatError, 'Found non-header line .*: ""'), ('phylip_invalid_empty_line_after_header', PhylipFormatError, 'Empty lines are not allowed.'), ('phylip_invalid_empty_line_before_header', PhylipFormatError, 'Found non-header line .*: ""'), ('phylip_invalid_empty_line_between_seqs', PhylipFormatError, 'Empty lines are not allowed.'), ('phylip_invalid_header_too_long', PhylipFormatError, 'Found non-header line .*: "2 20 extra_text"'), ('phylip_invalid_header_too_short', PhylipFormatError, 'Found non-header line .*: " 20"'), ('phylip_invalid_no_header', PhylipFormatError, 'Found non-header line .*: "foo .*"'), ('phylip_invalid_seq_too_long', PhylipFormatError, 'The length of sequence foo is not 20 as specified .*.'), ('phylip_invalid_seq_too_short', PhylipFormatError, 'The length of sequence foo is not 20 as specified .*.'), ('phylip_invalid_too_few_seqs', PhylipFormatError, 'The number of sequences is not .* as specified .*.'), ('phylip_invalid_too_many_seqs', PhylipFormatError, 'The number of sequences is not .* as specified in the header.'), ('phylip_invalid_zero_seq_len', PhylipFormatError, 'The number of sequences and the length must be positive.'), ('phylip_invalid_zero_seqs', PhylipFormatError, 'The number of sequences and the length must be positive.'), ]] def test_phylip_to_tabular_msa_invalid_files(self): for fp, error_type, error_msg_regex in self.invalid_files: with self.assertRaisesRegex(error_type, error_msg_regex): _phylip_to_tabular_msa(fp, constructor=DNA) def test_phylip_to_tabular_msa_no_constructor(self): with self.assertRaisesRegex(ValueError, '`constructor`'): _phylip_to_tabular_msa(get_data_path('phylip_dna_3_seqs')) def test_phylip_to_tabular_msa_valid_files(self): for valid_files, components in self.valid_configurations: for valid in valid_files: observed = _phylip_to_tabular_msa(valid, constructor=DNA) expected_seqs = [] expected_index = [] for seq, ID in components: expected_seqs.append(DNA(seq)) expected_index.append(ID) expected = TabularMSA(expected_seqs, index=expected_index) self.assertEqual(observed, expected) class TestWriters(unittest.TestCase): def setUp(self): # ids all same length, seqs longer than 10 chars dna_3_seqs = TabularMSA([ DNA('..ACC-GTTGG..', metadata={'id': "d1"}), DNA('TTACCGGT-GGCC', metadata={'id': "d2"}), DNA('.-ACC-GTTGC--', metadata={'id': "d3"})], minter='id') # id lengths from 0 to 10, with mixes of numbers, characters, and # spaces. sequences are shorter than 10 chars variable_length_ids = TabularMSA([ DNA('.-ACGT', metadata={'id': ''}), DNA('TGCA-.', metadata={'id': 'a'}), DNA('.ACGT-', metadata={'id': 'bb'}), DNA('TGCA-.', metadata={'id': '1'}), DNA('AAAAAA', metadata={'id': 'abcdefghij'}), DNA('GGGGGG', metadata={'id': 'ab def42ij'})], minter='id') # sequences with 20 chars = exactly two chunks of size 10 two_chunks = TabularMSA([ DNA('..ACC-GTTGG..AATGC.C', metadata={'id': 'foo'}), DNA('TTACCGGT-GGCCTA-GCAT', metadata={'id': 'bar'})], minter='id') # single sequence with more than two chunks single_seq_long = TabularMSA([ DNA('..ACC-GTTGG..AATGC.C----', metadata={'id': 'foo'})], minter='id') # single sequence with only a single character (minimal writeable # alignment) single_seq_short = TabularMSA([DNA('-', metadata={'id': ''})], minter='id') # alignments that can be written in phylip format self.objs = [dna_3_seqs, variable_length_ids, two_chunks, single_seq_long, single_seq_short] self.fps = map(get_data_path, ['phylip_dna_3_seqs', 'phylip_variable_length_ids', 'phylip_two_chunks', 'phylip_single_seq_long', 'phylip_single_seq_short']) # alignments that cannot be written in phylip format, paired with their # expected error message regexps self.invalid_objs = [ # no seqs (TabularMSA([]), 'one sequence'), # no positions (TabularMSA([DNA('', metadata={'id': "d1"}), DNA('', metadata={'id': "d2"})]), 'one position'), # ids too long (TabularMSA([RNA('ACGU', metadata={'id': "foo"}), RNA('UGCA', metadata={'id': "alongsequenceid"})], minter='id'), '10.*alongsequenceid') ] def test_write(self): for fp, obj in zip(self.fps, self.objs): fh = io.StringIO() _tabular_msa_to_phylip(obj, fh) obs = fh.getvalue() fh.close() with io.open(fp) as fh: exp = fh.read() self.assertEqual(obs, exp) def test_write_invalid_alignment(self): for invalid_obj, error_msg_regexp in self.invalid_objs: fh = io.StringIO() with self.assertRaisesRegex(PhylipFormatError, error_msg_regexp): _tabular_msa_to_phylip(invalid_obj, fh) # ensure nothing was written to the file before the error was # thrown obs = fh.getvalue() fh.close() self.assertEqual(obs, '') if __name__ == '__main__': unittest.main()