def setUp(self):
self.rvf = RepVariationFinder()
class Test_countVariationInMatrix(unittest.TestCase):
''' Test for file input to RepVariationFinder.countVariationInMatrix() '''
def setUp(self):
self.rvf = RepVariationFinder()
def test_noDiff(self):
matrix = '''
matrix
sp1 AACTGC
sp2 AACTGC
sp3 AACTGC
;
'''
contents = cStringIO.StringIO(matrix)
count = self.rvf.countVariationInMatrix(contents)
self.assertEquals(count, 0)
def test_oneDiff(self):
matrix = '''
matrix
sp1 AACTGC
sp2 ACCTGC
sp3 AACTGC
;
'''
contents = cStringIO.StringIO(matrix)
count = self.rvf.countVariationInMatrix(contents)
self.assertEquals(count, 1)
def test_allDiff(self):
matrix = '''
matrix
sp1 AACCCC
sp2 ACCTGT
sp3 TAGTGC
;
'''
contents = cStringIO.StringIO(matrix)
count = self.rvf.countVariationInMatrix(contents)
self.assertEquals(count, 6)
def test_remainderAfterCount(self):
matrix = '''
this shouldn't matter
matrix
sp1 AACCCC
sp2 ACCTGT
sp3 TAGTGC
;
This should be preserved
'''
contents = cStringIO.StringIO(matrix)
self.rvf.countVariationInMatrix(contents)
self.assertEquals('This should be preserved', contents.read().strip())
class Test_write(unittest.TestCase):
def setUp(self):
self.rvf = RepVariationFinder()
def test_noDiffs(self):
matrix = '''
begin data
[tree 1]
Matrix
sp1 AACTGC
sp2 AACTGC
sp3 AACTGC
;
begin data
[tree 2]
Matrix
sp1 TCGA
sp2 TCGA
sp3 TCGA
;
begin data
[tree 3]
Matrix
sp1 CGTCAA
sp2 CGTCAA
sp3 CGTCAA
;
'''
matrix2 = '''
[Variable Sites: 0]
begin data
[tree 1]
Matrix
sp1 AACTGC
sp2 AACTGC
sp3 AACTGC
;
[Variable Sites: 0]
begin data
[tree 2]
Matrix
sp1 TCGA
sp2 TCGA
sp3 TCGA
;
[Variable Sites: 0]
begin data
[tree 3]
Matrix
sp1 CGTCAA
sp2 CGTCAA
sp3 CGTCAA
;
'''
contents_in = cStringIO.StringIO(matrix)
contents_out = cStringIO.StringIO()
self.rvf.read(contents_in)
self.rvf.write(contents_out)
contents_out.seek(0)
results = contents_out.read()
# self.assertEqual(results, matrix)
self.assertMultiLineEqual(results, matrix2)
def test_severalDiffs(self):
matrix = '''
begin data
[tree 1]
Matrix
sp1 ATCTGC
sp2 AACTGC
sp3 AACTGC
;
begin data
[tree 2]
Matrix
sp1 TCGA
sp2 GACA
sp3 TCGT
;
begin data
[tree 3]
Matrix
sp1 CGTCAG
sp2 CGTCAA
sp3 TGTCCA
;
'''
matrix2 = '''
[Variable Sites: 4]
begin data
[tree 2]
Matrix
sp1 TCGA
sp2 GACA
sp3 TCGT
;
[Variable Sites: 3]
begin data
[tree 3]
Matrix
sp1 CGTCAG
sp2 CGTCAA
sp3 TGTCCA
;
[Variable Sites: 1]
begin data
[tree 1]
Matrix
sp1 ATCTGC
sp2 AACTGC
sp3 AACTGC
;
'''
contents_in = cStringIO.StringIO(matrix)
contents_out = cStringIO.StringIO()
self.rvf.read(contents_in)
self.rvf.write(contents_out)
contents_out.seek(0)
results = contents_out.read()
self.assertMultiLineEqual(results, matrix2)
def test_ignoreOutsideMatrix(self):
file_in = '''this should be ignored
begin data
[tree 1]
Matrix
sp1 ATCTGC
sp2 AACTGC
sp3 AACTGC
;
; some stuff
more stuff
begin data
[tree 2]
Matrix
sp1 TCGA
sp2 GACA
sp3 TCGT
;
; This should be ok too: MATRIX
begin data
[tree 3]
Matrix
sp1 CGTCAG
sp2 CGTCAA
sp3 TGTCCA
;
more crap at the end
'''
file_out = '''this should be ignored
[Variable Sites: 4]
begin data
[tree 2]
Matrix
sp1 TCGA
sp2 GACA
sp3 TCGT
;
; This should be ok too: MATRIX
[Variable Sites: 3]
begin data
[tree 3]
Matrix
sp1 CGTCAG
sp2 CGTCAA
sp3 TGTCCA
;
more crap at the end
[Variable Sites: 1]
begin data
[tree 1]
Matrix
sp1 ATCTGC
sp2 AACTGC
sp3 AACTGC
;
; some stuff
more stuff
'''
contents_in = cStringIO.StringIO(file_in)
contents_out = cStringIO.StringIO()
self.rvf.read(contents_in)
self.rvf.write(contents_out)
contents_out.seek(0)
results = contents_out.read()
self.assertEqual(self.rvf._startByte, 23)
self.assertMultiLineEqual(results, file_out)
class Test_read(unittest.TestCase):
''' Test for file input RepVariationFinder.read '''
def setUp(self):
self.rvf = RepVariationFinder()
def test_initialConfig(self):
self.assertEquals(len(self.rvf.replicateToCount), 0)
def test_byteCount(self):
matrix = '''begin data
Matrix
sp1 AACTGC
sp2 AACTGC
sp3 AACTGC
;
begin data
Matrix
sp1 TCGA
sp2 TCGA
sp3 TCGA
;
begin data
Matrix
sp1 CGTCAA
sp2 CGTCAA
sp3 CGTCAA
;
'''
contents = cStringIO.StringIO(matrix)
self.rvf.read(contents)
self.assertEquals(contents.tell() - 1,
self.rvf.replicateToLocation[2][1])
def test_noDiffs(self):
matrix = '''
begin data
Matrix
sp1 AACTGC
sp2 AACTGC
sp3 AACTGC
;
begin data
Matrix
sp1 TCGA
sp2 TCGA
sp3 TCGA
;
begin data
Matrix
sp1 CGTCAA
sp2 CGTCAA
sp3 CGTCAA
;
'''
contents = cStringIO.StringIO(matrix)
self.rvf.read(contents)
compare = {0: 0, 1: 0, 2: 0}
self.assertDictEqual(self.rvf.replicateToCount, compare)
def test_severalDiffs(self):
matrix = '''
begin data
Matrix
sp1 ATCTGC
sp2 AACTGC
sp3 AACTGC
;
begin data
Matrix
sp1 TCGA
sp2 GACA
sp3 TCGT
;
begin data
Matrix
sp1 CGTCAG
sp2 CGTCAA
sp3 TGTCCA
;
'''
contents = cStringIO.StringIO(matrix)
self.rvf.read(contents)
compare = {0: 1, 1: 4, 2: 3}
self.assertDictEqual(self.rvf.replicateToCount, compare)
def test_ignoreOutsideMatrix(self):
matrix = ''' this should be ignored
begin data
blah blah
Matrix
sp1 ATCTGC
sp2 AACTGC
sp3 AACTGC
;
; some stuff
more stuff
begin data
blah2 blah2
Matrix
sp1 TCGA
sp2 GACA
sp3 TCGT
;
; This should be ok too: MATRIX
begin data
blah3 blah3
Matrix
sp1 CGTCAG
sp2 CGTCAA
sp3 TGTCCA
;
more crap at the end
'''
contents = cStringIO.StringIO(matrix)
self.rvf.read(contents)
compare = {0: 1, 1: 4, 2: 3}
self.assertDictEqual(self.rvf.replicateToCount, compare)
