def test_alignment_to_clustal_with_bad_input(self):
BAD = StringIO('\n'.join(['dshfjsdfhdfsj', 'hfsdjksdfhjsdf']))
result = _clustal_to_alignment(BAD, strict=False)
self.assertEqual(dict(result), {})
# should fail unless we turned strict processing off
with self.assertRaises(ClustalFormatError):
BAD.seek(0)
dict(_clustal_to_alignment(BAD))
def test_alignment_to_clustal_with_bad_input(self):
BAD = StringIO('\n'.join(['dshfjsdfhdfsj', 'hfsdjksdfhjsdf']))
result = _clustal_to_alignment(BAD, strict=False)
self.assertEqual(dict(result), {})
# should fail unless we turned strict processing off
with self.assertRaises(ClustalFormatError):
BAD.seek(0)
dict(_clustal_to_alignment(BAD))
def test_valid_alignment_to_clustal_and_clustal_to_alignment(self):
import os
for valid_out in self.valid_clustal_out:
fname = "test.aln"
testfile = open(fname, 'w')
result_before = _clustal_to_alignment(valid_out)
_alignment_to_clustal(result_before, testfile)
testfile.close()
testfile = open(fname, 'r')
result_after = _clustal_to_alignment(testfile)
self.assertEquals(result_before, result_after)
os.remove(fname)
def test_valid_alignment_to_clustal_and_clustal_to_alignment(self):
import os
for valid_out in self.valid_clustal_out:
fname = "test.aln"
testfile = open(fname, 'w')
result_before = _clustal_to_alignment(valid_out)
_alignment_to_clustal(result_before, testfile)
testfile.close()
testfile = open(fname, 'r')
result_after = _clustal_to_alignment(testfile)
self.assertEquals(result_before, result_after)
os.remove(fname)
def test_invalid_alignment_to_clustal_and_clustal_to_alignment(self):
for invalid_out in self.invalid_clustal_out:
with self.assertRaises(ClustalFormatError):
dict(_clustal_to_alignment(invalid_out, strict=True))
def test_alignment_to_clustal_with_empty_input(self):
result = _clustal_to_alignment(StringIO())
self.assertEqual(dict(result), {})
def test_invalid_alignment_to_clustal_and_clustal_to_alignment(self):
for invalid_out in self.invalid_clustal_out:
with self.assertRaises(ClustalFormatError):
dict(_clustal_to_alignment(invalid_out, strict=True))
def test_alignment_to_clustal_with_empty_input(self):
result = _clustal_to_alignment(StringIO())
self.assertEqual(dict(result), {})