def test_cmbuild_from_alignment(self):
"""cmbuild_from_alignment should work as expected.
"""
#Test unaligned seqs and unaligned struct fail.
#DataError should be raised with Alignment is constructed
self.assertRaises(DataError,cmbuild_from_alignment,\
self.seqs1_unaligned,self.struct1_unaligned_string)
#Test aligned seqs and unaligned struct fail.
self.assertRaises(ValueError,cmbuild_from_alignment,\
self.seqs2_aligned,self.struct1_unaligned_string)
#Test get cm back without alignment.
cm_res = cmbuild_from_alignment(self.seqs2_aligned,\
self.struct2_aligned_string)
cm_lines = cm_res.split('\n')
ALN1_CM_lines = ALN1_CM.split('\n')
#Check that the same number of lines are in both CMs
self.assertEqual(len(cm_lines),len(ALN1_CM_lines))
#The first 13 lines are unique to the specific run. The res of the
# CM should be the same, since built from the same data.
self.assertEqual(cm_lines[13:],ALN1_CM_lines[13:])
#Make sure same alignment is returned if return_alignment=True
cm_res, cm_aln = cmbuild_from_alignment(self.seqs2_aligned,\
self.struct2_aligned_string,return_alignment=True)
self.assertEqual(cm_aln,self.lines2)
def test_cmbuild_from_file(self):
"""cmbuild_from_file should work as expected.
"""
cm_res = cmbuild_from_file(self.temp_dir+'/seqs1.sto')
cm_lines = cm_res.split('\n')
ALN1_CM_lines = ALN1_CM.split('\n')
#Check that the same number of lines are in both CMs
self.assertEqual(len(cm_lines),len(ALN1_CM_lines))
#The first 13 lines are unique to the specific run. The res of the
# CM should be the same, since built from the same data.
self.assertEqual(cm_lines[13:],ALN1_CM_lines[13:])
#Make sure same alignment is returned if return_alignment=True
cm_res, cm_aln = cmbuild_from_alignment(self.seqs2_aligned,\
self.struct2_aligned_string,return_alignment=True)
self.assertEqual(cm_aln,self.lines2)