def check(self, sequence, expected, dbParams=None):
"""
Check that, given a read with the sequence in C{sequence}, a
C{THAlphaHelix} finder finds all the helices given in C{expected}.
@param sequence: A C{str} of amino acids.
@param expected: A C{str}, consisting of '-' and 'H' characters, where
spans of 'H' characters indicate where helices are expected to be
found in C{sequence}. (The non-'H' characters do not have to be
hyphens, use whatever you like that is not an 'H'.)
@param dbParams: A C{DatabaseParameters} instance or C{None} if default
parameters should be used. This can be used to pass a non-default
featureLengthBase.
"""
self.assertEqual(len(sequence), len(expected))
read = AARead('id', sequence)
finder = THAlphaHelix(dbParams)
featureLengthBase = finder._dbParams.featureLengthBase
expectedHelices = []
for symbol, start, end in stringSpans(expected):
if symbol == 'H':
length = end - start
detail = scaleLog(length, featureLengthBase)
expectedHelices.append(
Landmark('THAlphaHelix', 'THA', start, length, detail))
self.assertEqual(expectedHelices, list(finder.find(read)))
def testAllLengthOne(self):
"""
A string whose spans are all of length one should give the expected
result.
"""
self.assertEqual([('a', 0, 1), ('b', 1, 2), ('c', 2, 3), ('d', 3, 4)],
list(stringSpans('abcd')))
def find(self, read):
"""
Find landmarks based on known secondary structures.
@param read: An instance of C{dark.reads.SSAARead}.
@return: A generator that yields C{Landmark} instances.
"""
for letter, start, end in stringSpans(read.structure):
if letter == self.STRUCTURE_LETTER:
yield Landmark(self.NAME, self.SYMBOL, start, end - start)
def testTwoSpans(self):
"""
A string with two spans should give the expected result.
"""
self.assertEqual([('a', 0, 4), ('b', 4, 6)],
list(stringSpans('aaaabb')))
def testIdentical(self):
"""
A string consists of just one character should give one span.
"""
self.assertEqual([('a', 0, 4)], list(stringSpans('aaaa')))
def testEmpty(self):
"""
An empty string has no spans.
"""
self.assertEqual([], list(stringSpans('')))