def testExpectedRecombinant(self):
"""
If a line of the recombinants is syntactically correct, the expected
Recombinant instance must be returned.
"""
mockOpener = mockOpen(read_data='\n'.join((
_RECOMBINANTS_HEADER,
'id1 id2 id3 0 1 6 1.0 1 3.0 5.0 4.0 6 '.replace(' ', '\t') +
' 1-3 & 4-6\t10-12 & 50-62',
)) + '\n')
with patch.object(builtins, 'open', mockOpener):
(recombinant, ) = list(readRecombinants('file.rec'))
self.assertEqual('id1', recombinant.pId)
self.assertEqual('id2', recombinant.qId)
self.assertEqual('id3', recombinant.recombinantId)
self.assertEqual(0, recombinant.m)
self.assertEqual(1, recombinant.n)
self.assertEqual(6, recombinant.k)
self.assertEqual(1.0, recombinant.p)
self.assertEqual(True, recombinant.hs)
self.assertEqual(3.0, recombinant.logp)
self.assertEqual(4.0, recombinant.dsP)
self.assertEqual(6, recombinant.minRecLength)
self.assertEqual((((1, 3), (4, 6)), ((10, 12), (50, 62))),
recombinant.breakpoints)
def testNoRecombinants(self):
"""
If the recombinants file has only a header, the readRecombinants
function must not yield any results.
"""
mockOpener = mockOpen(read_data=('%s\n' % _RECOMBINANTS_HEADER))
with patch.object(builtins, 'open', mockOpener):
self.assertEqual([], list(readRecombinants('filename')))
def testUnrecognizedHeader(self):
"""
If an unrecognized header line is passed, readRecombinants must
raise a ValueError.
"""
mockOpener = mockOpen(read_data='bad header\n')
with patch.object(builtins, 'open', mockOpener):
error = '^Unrecognized header line: bad header$'
assertRaisesRegex(self, ValueError, error, list,
readRecombinants('filename'))
def testInsufficientFields(self):
"""
If a line of the recombinants has less than 13 fields, a ValueError
must be raised.
"""
mockOpener = mockOpen(read_data='\n'.join((_RECOMBINANTS_HEADER,
'only\tthree\tfields')) +
'\n')
with patch.object(builtins, 'open', mockOpener):
error = r'^not enough values to unpack \(expected 13, got 3\)$'
assertRaisesRegex(self, ValueError, error, list,
readRecombinants('filename'))
def testNoBreakpointsOnLine(self):
"""
If a line of the recombinants has no breakpoint information, a
ValueError must be raised.
"""
mockOpener = mockOpen(read_data='\n'.join((
_RECOMBINANTS_HEADER,
'id1 id2 id3 0 0 6 1.0 1 3.0 4.0 4.0 6 '.replace(' ', '\t'),
)) + '\n')
with patch.object(builtins, 'open', mockOpener):
error = r"^No breakpoints found on line 2 of file\.rec$"
assertRaisesRegex(self, ValueError, error, list,
readRecombinants('file.rec'))
def testMinRecLengthNotAnInt(self):
"""
If a line of the recombinants has a minimum recombinant length value
that is not an int, a ValueError must be raised.
"""
mockOpener = mockOpen(read_data='\n'.join((
_RECOMBINANTS_HEADER,
'id1 id2 id3 0 0 6 1.0 1 3.0 4.0 4.0 six ...'.replace(' ', '\t'),
)) + '\n')
with patch.object(builtins, 'open', mockOpener):
error = r"^invalid literal for int\(\) with base 10: 'six'$"
assertRaisesRegex(self, ValueError, error, list,
readRecombinants('filename'))
def testDsPNotAFloat(self):
"""
If a line of the recombinants has a DS(p) value that is not a float, a
ValueError must be raised.
"""
mockOpener = mockOpen(read_data='\n'.join((
_RECOMBINANTS_HEADER,
'id1 id2 id3 0 0 0 6 1 4.0 4.0 six 5 ...'.replace(' ', '\t'),
)) + '\n')
with patch.object(builtins, 'open', mockOpener):
error = r"^could not convert string to float: 'six'$"
assertRaisesRegex(self, ValueError, error, list,
readRecombinants('filename'))
def testHSNotZeroOrOne(self):
"""
If a line of the recombinants has an hs value that is not '0' or '1', a
KeyError must be raised.
"""
mockOpener = mockOpen(read_data='\n'.join((
_RECOMBINANTS_HEADER,
'id1 id2 id3 0 0 0 3.1 x 3.0 4.0 4.0 5 ...'.replace(' ', '\t'),
)) + '\n')
with patch.object(builtins, 'open', mockOpener):
error = r"^'x'$"
assertRaisesRegex(self, KeyError, error, list,
readRecombinants('filename'))
def testBreakpointRight2NotInteger(self):
"""
If a line of the recombinants has a fourth breakpoint index a
non-integer, a ValueError must be raised.
"""
mockOpener = mockOpen(read_data='\n'.join((
_RECOMBINANTS_HEADER,
'id1 id2 id3 0 0 6 1.0 1 3.0 4.0 4.0 6 '.replace(' ', '\t') +
'2-3 & 4-a',
)) + '\n')
with patch.object(builtins, 'open', mockOpener):
error = r"^invalid literal for int\(\) with base 10: 'a'$"
assertRaisesRegex(self, ValueError, error, list,
readRecombinants('file.rec'))
def testBreakpointIndicesDescendingAcrossPair(self):
"""
If a line of the recombinants has breakpoint indices that
are descending across a pair of indices, a ValueError must be raised.
"""
mockOpener = mockOpen(read_data='\n'.join((
_RECOMBINANTS_HEADER,
'id1 id2 id3 0 0 6 1.0 1 3.0 4.0 4.0 6 '.replace(' ', '\t') +
'1-5 & 4-6',
)) + '\n')
with patch.object(builtins, 'open', mockOpener):
error = (r"^Breakpoints \(1-5 & 4-6\) on line 2 of file.rec "
r"do not have non-descending indices$")
assertRaisesRegex(self, ValueError, error, list,
readRecombinants('file.rec'))
def testTwoExpectedRecombinants(self):
"""
If two lines of recombinants are syntactically correct, the expected
Recombinant instances must be returned.
"""
mockOpener = mockOpen(read_data='\n'.join((
_RECOMBINANTS_HEADER,
'id1 id2 id3 0 1 6 1.0 1 3.0 5.0 4.0 6 '.replace(' ', '\t') +
' 1-3 & 4-6\t10-12 & 50-62',
'id4 id5 id6 1 2 7 2.0 0 4.0 6.0 5.0 7 '.replace(' ', '\t') +
' 2-4 & 5-7\t11-13 & 51-63',
)) + '\n')
with patch.object(builtins, 'open', mockOpener):
(recombinant1, recombinant2) = list(readRecombinants('file.rec'))
self.assertEqual('id1', recombinant1.pId)
self.assertEqual('id2', recombinant1.qId)
self.assertEqual('id3', recombinant1.recombinantId)
self.assertEqual(0, recombinant1.m)
self.assertEqual(1, recombinant1.n)
self.assertEqual(6, recombinant1.k)
self.assertEqual(1.0, recombinant1.p)
self.assertEqual(True, recombinant1.hs)
self.assertEqual(3.0, recombinant1.logp)
self.assertEqual(4.0, recombinant1.dsP)
self.assertEqual(6, recombinant1.minRecLength)
self.assertEqual((((1, 3), (4, 6)), ((10, 12), (50, 62))),
recombinant1.breakpoints)
self.assertEqual('id4', recombinant2.pId)
self.assertEqual('id5', recombinant2.qId)
self.assertEqual('id6', recombinant2.recombinantId)
self.assertEqual(1, recombinant2.m)
self.assertEqual(2, recombinant2.n)
self.assertEqual(7, recombinant2.k)
self.assertEqual(2.0, recombinant2.p)
self.assertEqual(False, recombinant2.hs)
self.assertEqual(4.0, recombinant2.logp)
self.assertEqual(5.0, recombinant2.dsP)
self.assertEqual(7, recombinant2.minRecLength)
self.assertEqual((((2, 4), (5, 7)), ((11, 13), (51, 63))),
recombinant2.breakpoints)