def testFindWithoutMotif(self):
"""
The find method must return an empty generator when no motif is
present.
"""
read = AARead('id', 'FFFFFFFFFFFFFFFFFFFFFFFFFFF')
finder = EukaryoticLinearMotif()
result = list(finder.find(read))
self.assertEqual([], result)
def testFindOneMotifMiddle(self):
"""
The find method must find a motif in the middle of a sequence.
"""
read = AARead('id', 'AAAAAAAAEKENLGYAAAAAAAA')
finder = EukaryoticLinearMotif()
result = list(finder.find(read))
self.assertEqual([
Landmark('EukaryoticLinearMotif', 'ELM', 8, 5, 'DEG_APCC_KENBOX_2')
], result)
def testFindOneMotifBeginning(self):
"""
The find method must find one motif at the beginning of a sequence.
"""
read = AARead('id', 'EKENLGYAAAAAAAA')
finder = EukaryoticLinearMotif()
result = list(finder.find(read))
self.assertEqual([
Landmark('EukaryoticLinearMotif', 'ELM', 0, 5, 'DEG_APCC_KENBOX_2')
], result)
def testFindOneMotifEnd(self):
"""
The find method must find a motif at the end of a sequence.
"""
read = AARead('id', 'AAAAAAAAEGGKENY')
finder = EukaryoticLinearMotif()
result = list(finder.find(read))
self.assertEqual([
Landmark('EukaryoticLinearMotif', 'ELM', 10, 5,
'DEG_APCC_KENBOX_2')
], result)
def testFindTwoIdenticalMotifsAdjacent(self):
"""
The find method must find two identical motifs next to each other.
"""
read = AARead('id', 'EKENLGKENG')
finder = EukaryoticLinearMotif()
result = list(finder.find(read))
self.assertEqual([
Landmark('EukaryoticLinearMotif', 'ELM', 0, 5,
'DEG_APCC_KENBOX_2'),
Landmark('EukaryoticLinearMotif', 'ELM', 5, 5, 'DEG_APCC_KENBOX_2')
], result)
def testFindTwoIdenticalMotifsNotAdjacent(self):
"""
The find method must find repeating identical motifs.
"""
read = AARead('id', 'EKENLGYAAAAAAAAEGKENGY')
finder = EukaryoticLinearMotif()
result = list(finder.find(read))
self.assertEqual([
Landmark('EukaryoticLinearMotif', 'ELM', 0, 5,
'DEG_APCC_KENBOX_2'),
Landmark('EukaryoticLinearMotif', 'ELM', 16, 5,
'DEG_APCC_KENBOX_2')
], result)
def testThreeDifferentMotifs(self):
"""
The find method must find two different motifs.
"""
read = AARead('id', 'EKENLGKENGWWWPWWP')
finder = EukaryoticLinearMotif()
result = list(finder.find(read))
self.assertEqual([
Landmark('EukaryoticLinearMotif', 'ELM', 0, 5,
'DEG_APCC_KENBOX_2'),
Landmark('EukaryoticLinearMotif', 'ELM', 5, 5,
'DEG_APCC_KENBOX_2'),
Landmark('EukaryoticLinearMotif', 'ELM', 10, 4, 'LIG_CSL_BTD_1'),
Landmark('EukaryoticLinearMotif', 'ELM', 10, 7, 'LIG_SH3_3')
], result)
def testMatchAlteration(self):
"""
The find method must work on a regex that contains alternation (e.g.,
[ABC]).
"""
# Make sure we know what pattern is actually being matched.
self.assertEqual('.P[TS]AP.', _DATABASE[22]['pattern'].pattern)
self.assertEqual('LIG_PTAP_UEV_1', _DATABASE[22]['identifier'])
finder = EukaryoticLinearMotif()
result = list(finder.find(AARead('id', 'SPTAPS')))
self.assertEqual(
[Landmark('EukaryoticLinearMotif', 'ELM', 0, 6, 'LIG_PTAP_UEV_1')],
result)
result = list(finder.find(AARead('id', 'SPSAPS')))
self.assertEqual(
[Landmark('EukaryoticLinearMotif', 'ELM', 0, 6, 'LIG_PTAP_UEV_1')],
result)