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