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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 string
from io import StringIO
from unittest import TestCase, main
from skbio import TabularMSA
from skbio.sequence._grammared_sequence import GrammaredSequence
from skbio.util._decorator import classproperty, overrides
from skbio.io.format.clustal import (
_clustal_to_tabular_msa, _tabular_msa_to_clustal, _clustal_sniffer,
_is_clustal_seq_line, _delete_trailing_number, _check_length,
_label_line_parser)
from skbio.io import ClustalFormatError
class CustomSequence(GrammaredSequence):
@classproperty
@overrides(GrammaredSequence)
def gap_chars(cls):
return set('-.')
@classproperty
@overrides(GrammaredSequence)
def default_gap_char(cls):
return '-'
@classproperty
@overrides(GrammaredSequence)
def definite_chars(cls):
return set(string.ascii_letters)
@classproperty
@overrides(GrammaredSequence)
def degenerate_map(cls):
return {}
class ClustalHelperTests(TestCase):
def test_label_line_parser(self):
self.assertEqual(_label_line_parser(StringIO('abc\tucag')),
({"abc": ["ucag"]}, ['abc']))
with self.assertRaises(ClustalFormatError):
_label_line_parser(StringIO('abctucag'))
def test_is_clustal_seq_line(self):
ic = _is_clustal_seq_line
self.assertTrue(ic('abc'))
self.assertTrue(ic('abc def'))
self.assertFalse(ic('CLUSTAL'))
self.assertFalse(ic('CLUSTAL W fsdhicjkjsdk'))
self.assertFalse(ic(' * *'))
self.assertFalse(ic(' abc def'))
self.assertFalse(ic('MUSCLE (3.41) multiple sequence alignment'))
def test_delete_trailing_number(self):
dtn = _delete_trailing_number
self.assertEqual(dtn('abc'), 'abc')
self.assertEqual(dtn('a b c'), 'a b c')
self.assertEqual(dtn('a \t b \t c'), 'a \t b \t c')
self.assertEqual(dtn('a b 3'), 'a b')
self.assertEqual(dtn('a b c \t 345'), 'a b c')
def test_check_lengh(self):
self.assertEqual(False,
_check_length({'abc': ['adjfkadfjaksdlfadskfda'],
'xyz': ['adjfkadfjaksdlfadsk']},
['abc', 'xyz'])),
self.assertEqual(True,
_check_length({'abc': ['adjfkadfjaksdlfadskfda'],
'xyz': ['adjfkadfjaksdlfadsksdf']},
['abc', 'xyz']))
self.assertEqual(True,
_check_length({'abc': ['adjfkadfjaksdlfadskfda',
'adjfkadfjaksdlfadskfda'],
'xyz': ['adjfkadfjaksdlfadsksdf',
'adjfkadfjaksdlfadsksdf']},
['abc', 'xyz']))
self.assertEqual(False,
_check_length({'abc': ['adjfkadfjaksdlfadskfd',
'adjfkadfjaksdlfadskfda'],
'xyz': ['adjfkadfjaksdlfadsksdf',
'adjfkadfjaksdlfadsksdf']},
['abc', 'xyz']))
self.assertEqual(False,
_check_length({'abc': ['adjfkadfjaksdlfadskfda',
'adjfkadfjaksdlfadskfda'],
'xyz': ['adjfkadfjaksdlfadsksdf',
'adjfkadfjaksdlfadsksd']},
['abc', 'xyz']))
class ClustalIOTests(TestCase):
def setUp(self):
self.valid_clustal_out = [
StringIO('CLUSTAL\n\nabc\tucag'),
StringIO('CLUSTAL\n\nabc\tuuu\ndef\tccc\n\n ***\n\ndef ggg\nab'
'c\taaa\n'),
StringIO('\n'.join(['CLUSTAL\n', 'abc uca', 'def ggg ccc'])),
StringIO('\n'.join(['CLUSTAL\n', 'abc uca ggg', 'def ggg ccc'])),
StringIO("""CLUSTAL
abc GCAUGCAUGCAUGAUCGUACGUCAGCAUGCUAGACUGCAUACGUACGUACGCAUGCAUCA
def ------------------------------------------------------------
xyz ------------------------------------------------------------
"""),
StringIO("""CLUSTAL
abc GCAUGCAUGCAUGAUCGUACGUCAGCAUGCUAGACUGCAUACGUACGUACGCAUGCAUCA
def ------------------------------------------------------------
xyz ------------------------------------------------------------
abc GUCGAUACGUACGUCAGUCAGUACGUCAGCAUGCAUACGUACGUCGUACGUACGU-CGAC
def -----------------------------------------CGCGAUGCAUGCAU-CGAU
xyz -------------------------------------CAUGCAUCGUACGUACGCAUGAC
"""),
StringIO("""CLUSTAL W (1.82) multiple sequence alignment
abc GCAUGCAUGCAUGAUCGUACGUCAGCAUGCUAGACUGCAUACGUACGUACGCAUGCAUCA
def ------------------------------------------------------------
xyz ------------------------------------------------------------
abc GUCGAUACGUACGUCAGUCAGUACGUCAGCAUGCAUACGUACGUCGUACGUACGU-CGAC
def -----------------------------------------CGCGAUGCAUGCAU-CGAU
xyz -------------------------------------CAUGCAUCGUACGUACGCAUGAC
abc UGACUAGUCAGCUAGCAUCGAUCAGU
def CGAUCAGUCAGUCGAU----------
xyz UGCUGCAUCA----------------"""),
StringIO("""CLUSTAL W (1.74) multiple sequence alignment
abc GCAUGCAUGCAUGAUCGUACGUCAGCAUGCUAGACUGCAUACGUACGUACGCAUGCAUCA 60
def ------------------------------------------------------------
xyz ------------------------------------------------------------
abc GUCGAUACGUACGUCAGUCAGUACGUCAGCAUGCAUACGUACGUCGUACGUACGU-CGAC 11
def -----------------------------------------CGCGAUGCAUGCAU-CGAU 18
xyz -------------------------------------CAUGCAUCGUACGUACGCAUGAC 23
: * * * * **
abc UGACUAGUCAGCUAGCAUCGAUCAGU 145
def CGAUCAGUCAGUCGAU---------- 34
xyz UGCUGCAUCA---------------- 33
* ***""")
]
self.invalid_clustal_out = [StringIO('\n'.join(['dshfjsdfhdfsj',
'hfsdjksdfhjsdf'])),
StringIO('\n'.join(['hfsdjksdfhjsdf'])),
StringIO('\n'.join(['dshfjsdfhdfsj',
'dshfjsdfhdfsj',
'hfsdjksdfhjsdf'])),
StringIO('\n'.join(['dshfjsdfhdfsj',
'\t',
'hfsdjksdfhjsdf'])),
StringIO('\n'.join(['dshfj\tdfhdfsj',
'hfsdjksdfhjsdf'])),
StringIO('\n'.join(['dshfjsdfhdfsj',
'hfsdjk\tdfhjsdf'])),
StringIO("""CLUSTAL W (1.74) multiple sequence alignment
adj GCAUGCAUGCAUGAUCGUACGUCAGCAUGCUAGACUGCAUACGUACGUACGCAUGCAUCA
------------------------------------------------------------
adk -----GGGGGGG------------------------------------------------
"""),
StringIO("""CLUSTAL W (1.74) multiple sequence alignment
adj GCAUGCAUGCAUGAUCGUACGUCAGCAUGCUAGACUGCAUACGUACGUACGCAUGCAUCA
adk -----GGGGGGG------------------------------------------------
adj GCAUGCAUGCAUGAUCGUACGUCAGCAUGCUAGACUGCAUACGUACGUACGCAUGCAUCA
adk -----GGGGGGG---------------------------------------------
"""),
StringIO("""CLUSTAL W (1.74) multiple sequence alignment
adj GCAUGCAUGCAUGAUCGUACGUCAGCAUGCUAGACUGCAUACGUACGUACGCAUGCAUCA
adk -----GGGGGGG---------------------------------------------
adj GCAUGCAUGCAUGAUCGUACGUCAGCAUGCUAGACUGCAUACGUACGUACGCAUGCA
adk -----GGGGGGG---------------------------------------------
"""),
StringIO("""CLUSTAL W (1.74) multiple sequence alignment
adj GCAUGCAUGCAUGAUCGUACGUCAGCAUGCUAGACUGCAUACGUACGUACGCAUGCAUCA
------------------------------------------------------------
adk -----GGGGGGG------------------------------------------------
"""),
StringIO("""CLUSTAL W (1.74) multiple sequence alignment
GCAUGCAUGCAUGAUCGUACGUCAGCAUGCUAGACUGCAUACGUACGUACGCAUGCAUCA
------------------------------------------------------------
------------------------------------------------------------
GUCGAUACGUACGUCAGUCAGUACGUCAGCAUGCAUACGUACGUCGUACGUACGU-CGAC
-----------------------------------------CGCGAUGCAUGCAU-CGAU
------------------------------------------------------------
: * * * * **
UGACUAGUCAGCUAGCAUCGAUCAGU 145
CGAUCAGUCAGUCGAU---------- 34
UGCUGCAUCA---------------- 33
* ***""")]
def test_tabular_msa_to_clustal_with_empty_input(self):
result = _clustal_to_tabular_msa(StringIO(),
constructor=CustomSequence)
self.assertEqual(dict(result), {})
def test_tabular_msa_to_clustal_with_bad_input(self):
BAD = StringIO('\n'.join(['dshfjsdfhdfsj', 'hfsdjksdfhjsdf']))
with self.assertRaises(ClustalFormatError):
dict(_clustal_to_tabular_msa(BAD, constructor=CustomSequence))
def test_valid_tabular_msa_to_clustal_and_clustal_to_tabular_msa(self):
for valid_out in self.valid_clustal_out:
result_before = _clustal_to_tabular_msa(
valid_out, constructor=CustomSequence)
with StringIO() as fh:
_tabular_msa_to_clustal(result_before, fh)
fh.seek(0)
result_after = _clustal_to_tabular_msa(
fh, constructor=CustomSequence)
self.assertEqual(result_before, result_after)
def test_invalid_tabular_msa_to_clustal_and_clustal_to_tabular_msa(self):
for invalid_out in self.invalid_clustal_out:
with self.assertRaises(ClustalFormatError):
dict(_clustal_to_tabular_msa(invalid_out,
constructor=CustomSequence))
def test_clustal_sniffer_valid_files(self):
for valid_out in self.valid_clustal_out:
self.assertEqual(_clustal_sniffer(valid_out), (True, {}))
def test_clustal_sniffer_invalid_files(self):
for invalid_out in self.invalid_clustal_out:
self.assertEqual(_clustal_sniffer(invalid_out), (False, {}))
# sniffer should return False on empty file (which isn't contained
# in self.invalid_clustal_out since an empty file is a valid output)
self.assertEqual(_clustal_sniffer(StringIO()), (False, {}))
def test_no_constructor(self):
with self.assertRaisesRegex(ValueError, "`constructor`"):
_clustal_to_tabular_msa(self.valid_clustal_out[0])
def test_duplicate_labels(self):
msa = TabularMSA([CustomSequence('foo'),
CustomSequence('bar')], index=['a', 'a'])
with self.assertRaisesRegex(ClustalFormatError, "index.*unique"):
with StringIO() as fh:
_tabular_msa_to_clustal(msa, fh)
def test_invalid_lengths(self):
fh = StringIO(
"CLUSTAL\n"
"\n\n"
"abc GCAU\n"
"def -----\n")
with self.assertRaisesRegex(ClustalFormatError, "not aligned"):
_clustal_to_tabular_msa(fh, constructor=CustomSequence)
if __name__ == '__main__':
main()
|
