def test_clustal_from_alignment(self): """should return correct clustal string.""" self.assertEqual(clustal_from_alignment({}),'') self.assertEqual(clustal_from_alignment(self.alignment_dict),\ self.clustal_with_label) self.assertEqual(clustal_from_alignment(self.alignment_dict, interleave_len=2),self.clustal_with_label_lw2)
def test_clustal_from_alignment_reordered(self): """should return correct clustal string.""" self.assertEqual(clustal_from_alignment(self.alignment_object),\ self.clustal_with_label_reordered) self.assertEqual( clustal_from_alignment(self.alignment_object, interleave_len=2), self.clustal_with_label_lw2_reordered)
def rnaalifold_from_alignment(aln,moltype=RNA,params=None): """Returns seq, pairs, folding energy for alignment. """ #Create Alignment object. Object will handle if seqs are unaligned. aln = Alignment(aln,MolType=RNA) int_map, int_keys = aln.getIntMap() app = RNAalifold(WorkingDir='/tmp',\ InputHandler='_input_as_multiline_string',params=params) res = app(clustal_from_alignment(int_map)) #seq,pairs,energy = rnaalifold_parser(res['StdOut'].readlines()) pairs_list = MinimalRnaalifoldParser(res['StdOut'].readlines()) res.cleanUp() return pairs_list
def rnaalifold_from_alignment(aln, moltype=RNA, params=None): """Returns seq, pairs, folding energy for alignment. """ #Create Alignment object. Object will handle if seqs are unaligned. aln = Alignment(aln, MolType=RNA) int_map, int_keys = aln.getIntMap() app = RNAalifold(WorkingDir='/tmp',\ InputHandler='_input_as_multiline_string',params=params) res = app(clustal_from_alignment(int_map)) #seq,pairs,energy = rnaalifold_parser(res['StdOut'].readlines()) pairs_list = MinimalRnaalifoldParser(res['StdOut'].readlines()) res.cleanUp() return pairs_list
def test_clustal_from_alignment_reordered(self): """should return correct clustal string.""" self.assertEqual(clustal_from_alignment(self.alignment_object),\ self.clustal_with_label_reordered) self.assertEqual(clustal_from_alignment(self.alignment_object, interleave_len=2),self.clustal_with_label_lw2_reordered)