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)
