test_new.py 文件源码

def test_malign(self):

        self.setUpPhylotyper(aa=False)

        tmpfiles = [ os.path.join(self.test_dir, 'tmp1.fasta'),
            os.path.join(self.test_dir, 'tmp2.fasta')
        ]

        tmpfile = os.path.join(self.test_dir, 'tmp_saln.fasta')

        aln = SeqAligner(self.configObj)
        aln.malign(self.subtype_options['input'], tmpfiles, tmpfile)

        lengths = []
        tmpfiles.append(tmpfile)
        for f in tmpfiles:
            seqs = SeqIO.parse(open(f, 'r'),'fasta')
            lengths.append(len(str(seqs.next().seq)))

        self.assertEqual(lengths[0]+lengths[1], lengths[2])


    ## TODO Add test for new multi amino acid/dna