def test_count_node(self):
"""Count nodes in a SeqBDD"""
from seqbdd import SeqBDD
self.assertEqual(SeqBDD.empty().count_node(), 0)
self.assertEqual(SeqBDD.null().count_node(), 0)
self.assertEqual(SeqBDD(['aa', 'ab']).count_node(), 3)
def setUp(self):
from seqbdd import SeqBDD
self.seq1 = {'aa', 'ab'}
self.seq2 = {'aa', 'ac'}
self.sdd1 = SeqBDD(list(self.seq1))
self.sdd2 = SeqBDD(list(self.seq2))
def test_count(self):
"""Count sequences are contained in a SeqBDD"""
from seqbdd import SeqBDD
self.assertEqual(SeqBDD.empty().count(), 0)
self.assertEqual(SeqBDD.null().count(), 1)
self.assertEqual(SeqBDD(['ab', 'cd']).count(), 2)
def test_ne(self):
"""Work `!=` operation"""
from seqbdd import SeqBDD
sdd1 = SeqBDD(['aa', 'ab'])
sdd2 = SeqBDD(['aa', 'ab'])
sdd3 = SeqBDD(['aa', 'ac'])
self.assertFalse(sdd1 != sdd2)
self.assertTrue(sdd1 != sdd3)
def test_contains(self):
"""Work `in` statements"""
from seqbdd import SeqBDD
sdd = SeqBDD(['aa', 'ab'])
self.assertTrue('aa' in sdd)
self.assertFalse('ac' in sdd)
def test_suffixdd(self):
"""Get a SuffixDD"""
from seqbdd import SeqBDD
self.assertEqual(
SeqBDD.suffixdd('abc').values(),
['', 'a', 'ab', 'abc', 'b', 'bc', 'c'])
def test_glocal_alignment(self):
"""Align a sequence and a SeqBDD glocally"""
from seqbdd import SeqBDD
# http://www.uniprot.org/uniprot/Q8NHC7
sequence = (
'MPNSTTVMEFLLMRFSDVWTLQILHSASFFMLYLVTLMGNILIVTVTTCDSSLHMPMYFF'
'LRNLSILDACYISVTVPTSCVNSLLDSTTISKAGCVAQVFLVVFFVYVELLFLTIMAHDR'
'YVAVCQPLHYPVIVNSRICIQMTLASLLSGLVYAGMHTGSTFQLPFCRSNVIHQFFCDIP'
'SLLKLSCSDTFSNEVMIVVSALGVGGGCFIFIIRSYIHIFSTVLGFPRGADRTKAFSTCI'
'PHILVVSVFLSSCSSVYLRPPAIPAATQDLILSGFYSIMPPLFNPIIYSLRNKQIKVAIK'
'KIMKRIFYSENV')
query_sequences = ['NSTTVMEFLLMRF', 'IIYSLRNKQIKVA']
query = SeqBDD(query_sequences)
gapopen = 11
gapext = 1
p = 0.9
results = query.glocal_alignment(sequence, gapopen, gapext, p)
self.assertEqual(2, len(results))
self.assertEqual('NSTTVMEFLLMRF', results[0].sequence1)
self.assertEqual(sequence, results[0].sequence2)
self.assertEqual('NSTTVMEFLLMRF', results[0].aligned_sequence1)
self.assertEqual('NSTTVMEFLLMRF', results[0].aligned_sequence2)
self.assertEqual((0, 13), results[0].span_sequence1)
self.assertEqual((2, 15), results[0].span_sequence2)
self.assertEqual(64, results[0].score)
self.assertEqual('IIYSLRNKQIKVA', results[1].sequence1)
self.assertEqual(sequence, results[1].sequence2)
self.assertEqual('IIYSLRNKQIKVA', results[1].aligned_sequence1)
self.assertEqual('IIYSLRNKQIKVA', results[1].aligned_sequence2)
self.assertEqual((0, 13), results[1].span_sequence1)
self.assertEqual((285, 298), results[1].span_sequence2)
self.assertEqual(61, results[1].score)
def test_top(self):
"""Get the character of root node"""
from seqbdd import SeqBDD
self.assertEqual(SeqBDD.empty().top(), '0')
self.assertEqual(SeqBDD(['ab', 'cd']).top(), 'c')
def test_push(self):
"""Get a SeqBDD is pushed a character"""
from seqbdd import SeqBDD
self.assertEqual(
SeqBDD(['bc', 'bd']).push('a').values(), ['abc', 'abd'])
def test_onset(self):
"""Get an onset"""
from seqbdd import SeqBDD
self.assertEqual(SeqBDD(['bc', 'bd']).onset('b').values(), ['c', 'd'])
self.assertEqual(SeqBDD(['bc', 'bd']).onset('a').values(), [])
def test_null(self):
"""Generate a set only has empty sequence"""
from seqbdd import SeqBDD
self.assertEqual(SeqBDD.null().values(), [''])
def test_empty(self):
"""Generate the empty set"""
from seqbdd import SeqBDD
self.assertFalse(bool(SeqBDD.empty().values()))
def test_instance(self):
"""Generate an instance of the SeqBDD"""
from seqbdd import SeqBDD
self.assertEqual(SeqBDD(['a']).values(), ['a'])
def test_search(self):
"""Search a sequence by a SeqBDD"""
from seqbdd import SeqBDD
sdd = SeqBDD(['abc', 'def'])
self.assertEqual(sdd.search('abcdef'), [(0, 'abc'), (3, 'def')])
self.assertEqual(sdd.search('abcdefabcdef'), [(0, 'abc'), (3, 'def'),
(6, 'abc'), (9, 'def')])
sdd = SeqBDD(['ab', 'bc', 'bab', 'd', 'abcde'])
self.assertEqual(sdd.search('xbabcdex'), [(1, 'bab'), (2, 'ab'),
(2, 'abcde'), (3, 'bc'),
(5, 'd')])
self.assertEqual(sdd.search('abc'), [(0, 'ab'), (1, 'bc')])
self.assertEqual(sdd.search('ab'), [(0, 'ab')])
sdd = SeqBDD(['a', 'ab', 'bc', 'bca', 'c', 'caa'])
self.assertEqual(sdd.search('abccab'), [(0, 'a'), (0, 'ab'), (1, 'bc'),
(2, 'c'), (3, 'c'), (4, 'a'),
(4, 'ab')])