def setUp(self): self.qallbed = Bed("data/rice_v6_setaria64/rice_v6.all.bed", "data/rice_v6_setaria64/rice_v6.fasta") self.qallbed.fill_dict() self.sallbed = Bed("data/rice_v6_setaria64/setaria64.all.bed", "data/rice_v6_setaria64/setaria64.fasta") self.sallbed.fill_dict() self.saccn = self.sallbed.accn("Si000834m") blastfh = open("blast_res") self.blast = blastfh.read() self.d, self.pseudo = group_cds(self.blast, self.saccn)
def test_group_cds_2(self): blast_2fh = open("blast_2") blast_2 = blast_2fh.read() d, pseudo = group_cds(blast_2, self.sallbed.accn("Si002524m")) self.assertEqual(len(d.keys()), 5) for key in d.keys(): # logging.info('key: {0}'.format(key)) self.assertEqual(1, len(d[key]))