def test_fasta_from_alignment(self): """should return correct fasta string.""" self.assertEqual(fasta_from_alignment({}),'') self.assertEqual(fasta_from_alignment(self.alignment_dict),\ self.fasta_with_label) self.assertEqual(fasta_from_alignment(self.alignment_object),\ self.fasta_with_label)
def findMotifsFromAlignment(aln,WorkingDir=None): """Runs MEME using an Alignment object. - Returns MotifResults object - seqs can be an Alignment object or dict """ #Make Fasta Alignment fasta_aln = fasta_from_alignment(aln) #Make sure aln is Alignment object aln = Alignment(aln) app = MEME(InputHandler='_input_as_lines') output = app(fasta_aln) meme_results = MemeParser(output['StdOut']) meme_results.Alignment = aln return add_p_values(meme_results)