def __get_blastall_conf(self, jc): pu.jc_configure(self, jc, 'bl.mr.seq.blastall.exe', 'blastall_exe', '/usr/bin/blastall') pu.jc_configure(self, jc, 'bl.mr.seq.blastall.program', 'program', 'blastn') pu.jc_configure(self, jc, 'bl.mr.seq.blastall.db.name', 'db_name') pu.jc_configure_float(self, jc, 'bl.mr.seq.blastall.evalue', 'evalue', 1.0) pu.jc_configure_int(self, jc, 'bl.mr.seq.blastall.gap.cost', 'gap_cost', 1) pu.jc_configure_int(self, jc, 'bl.mr.seq.blastall.word.size', 'word_size', 20) pu.jc_configure_bool(self, jc, 'bl.mr.seq.blastall.filter', 'filter', False)
def __get_configuration(self, jc): pu.jc_configure(self, jc, 'bl.mr.seq.blastall.log.level', 'log_level', 'WARNING') try: self.log_level = getattr(logging, self.log_level) except AttributeError: raise ValueError("Unsupported log level: %r" % self.log_level) pu.jc_configure(self, jc, 'bl.mr.seq.blastall.exe', 'blastall_exe', '/usr/bin/blastall') pu.jc_configure(self, jc, 'bl.mr.seq.blastall.program', 'program', 'blastn') pu.jc_configure(self, jc, 'bl.mr.seq.blastall.db.name', 'db_name') pu.jc_configure_float(self, jc, 'bl.mr.seq.blastall.evalue', 'evalue', 1.0) pu.jc_configure_int(self, jc, 'bl.mr.seq.blastall.gap.cost', 'gap_cost', 1) pu.jc_configure_int(self, jc, 'bl.mr.seq.blastall.word.size', 'word_size', 20) pu.jc_configure_bool(self, jc, 'bl.mr.seq.blastall.filter', 'filter', False)
def test_jc_configure_plain(self): w = CONFIGURE_EXAMPLES d = {} for k in w.keys(): d[k] = w[k][1] jc = pp.get_JobConf_object(d) o = Obj() for k in w.keys(): self.assertTrue(jc.hasKey(k)) if w[k][0] == 'str': pu.jc_configure(o, jc, k, k) self.assertEqual(getattr(o,k), w[k][1]) elif w[k][0] == 'int': pu.jc_configure_int(o, jc, k, k) self.assertEqual(getattr(o, k), int(w[k][1])) elif w[k][0] == 'bool': pu.jc_configure_bool(o, jc, k, k) self.assertEqual(getattr(o, k), w[k][1] == 'true') elif w[k][0] == 'float': pu.jc_configure_float(o, jc, k, k) self.assertAlmostEqual(getattr(o, k), float(w[k][1])) elif w[k][0] == 'log_level': pu.jc_configure_log_level(o, jc, k, k) self.assertEqual(getattr(o, k), getattr(logging, w[k][1]))
def test_jc_configure_plain(self): w = CONFIGURE_EXAMPLES d = {} for k in w.keys(): d[k] = w[k][1] jc = pp.get_JobConf_object(d) o = Obj() for k in w.keys(): self.assertTrue(jc.hasKey(k)) if w[k][0] == 'str': pu.jc_configure(o, jc, k, k) self.assertEqual(getattr(o, k), w[k][1]) elif w[k][0] == 'int': pu.jc_configure_int(o, jc, k, k) self.assertEqual(getattr(o, k), int(w[k][1])) elif w[k][0] == 'bool': pu.jc_configure_bool(o, jc, k, k) self.assertEqual(getattr(o, k), w[k][1] == 'true') elif w[k][0] == 'float': pu.jc_configure_float(o, jc, k, k) self.assertAlmostEqual(getattr(o, k), float(w[k][1])) elif w[k][0] == 'log_level': pu.jc_configure_log_level(o, jc, k, k) self.assertEqual(getattr(o, k), getattr(logging, w[k][1]))
def __get_tiget_conf(self, jc): pu.jc_configure_int(self, jc, 'bl.mr.seq.tiget.max.hits', 'max_hits', 10) pu.jc_configure_int(self, jc, 'bl.mr.seq.tiget.max.start', 'max_start', 4) pu.jc_configure_float(self, jc, 'bl.mr.seq.tiget.min.identity.percent', 'min_identity', 95.0) pu.jc_configure_float(self, jc, 'bl.mr.seq.tiget.min.al2seq.percent', 'min_al2seq', 15.0) self.min_al2seq /= 100 pu.jc_configure_float(self, jc, 'bl.mr.seq.tiget.min.score.diff', 'min_score_diff', 20.0)