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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 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()
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