def main():
#print('Getting data')
#get_data()
print('Starting examinations')
# This and other code in this and other modules is sometimes a bit confusing
# because I use 'seq' for both just the integer of the sequence leader *and*
# the corresponding SequenceInfo object.
# data is a dictionary mapping the ints to the SequenceInfo objects.
data = SequencesManager(CONFIG)
data.readonly_init()
targets = []
derp = []
for i, seq in enumerate(data.values()):
#print('looking at seq {}'.format(i))
ress = filter_seq(seq)
if ress:
derp.append((seq, ress))
print('Getting details for {} seqs'.format(len(derp)))
for seq, ress in derp:
res = examine_seq(seq.id, None, *ress, seq)
if res:
targets.append((seq, res))
targets.sort(
key=lambda tup: (not tup[0].driver, tup[0].klass, tup[0].cofactor)
) # Drivers first, then sort by class first, secondary sort by comp size
for seq, ress in targets:
for res in ress:
print("{:>6} ~ {} (class {}) maybe: {}".format(
seq.seq, seq.guide, seq.klass,
aq.analyze_composite_tau_to_str(res, 'C' + str(seq.cofactor))))
def filter(filt_expr, sort_expr, N, sep):
filt = lambda ali: eval(filt_expr)
sort = lambda ali: eval(sort_expr)
seqinfo = SequencesManager(CONFIG)
seqinfo.readonly_init()
out = [ali for ali in seqinfo.values() if filt(ali)]
out.sort(key=sort)
out = out[:N]
#print('\n'.join("{}: {}, {}".format(ali.seq, filt(ali), sort(ali)) for ali in out))
print(sep.join(str(ali.seq) for ali in out))
def main():
err = "Error: commands are 'add', 'drop', or 'spider'"
if len(argv) < 2:
print(err)
exit(-1)
s = SequencesManager(CONFIG)
with s.acquire_lock(block_minutes=CONFIG['blockminutes']): # reads and inits
inner_main(s, err)
def main():
err = "Error: commands are 'add', 'drop', or 'spider'"
if len(argv) < 2:
print(err)
exit(-1)
s = SequencesManager(CONFIG)
with s.acquire_lock(
block_minutes=CONFIG['blockminutes']): # reads and inits
inner_main(s, err)
def main():
seqsmanager = SequencesManager(CONFIG, _sequence_class=OldInfo)
with seqsmanager.acquire_lock(block_minutes=0):
LOGGER.info("seqsmanager inited, converting seq format...")
for seq, ali in seqsmanager.items():
# we use either ali.seq or ali[0], but for constructor use
# we need the attrs as dictionary keywords instead
dct = {kw: getattr(ali, kw) for kw in ali._map}
newali = SequenceInfo(**dct)
seqsmanager._data[seq] = newali
# adjust the following for the specifics of the new SequenceInfo
newali.set_abundance()
def main():
seqsmanager = SequencesManager(CONFIG, _sequence_class=OldInfo)
with seqsmanager.acquire_lock(block_minutes=0):
LOGGER.info("seqsmanager inited, converting seq format...")
for seq, ali in seqsmanager.items():
# we use either ali.seq or ali[0], but for constructor use
# we need the attrs as dictionary keywords instead
dct = {kw: getattr(ali, kw) for kw in ali._map}
newali = SequenceInfo(**dct)
seqsmanager._data[seq] = newali
# adjust the following for the specifics of the new SequenceInfo
newali.set_abundance()
def test_auto_lock_unlock(self):
seqinfo = SequencesManager(self.config)
self.assertFalse(exists(self.txtfile))
with seqinfo.acquire_lock(block_minutes=0):
self.assertTrue(seqinfo._have_lock)
self.assertTrue(exists(self.lockfile))
self.assertFalse(exists(self.txtfile))
self.assertFalse(exists(self.lockfile))
self.assertTrue(exists(self.txtfile))
self.assertFilesEqual(seqinfo.file, self.snapshot)
self.assertFilesEqual(self.txtfile, self.txtsnapshot)
def test_auto_lock_unlock(self):
seqinfo = SequencesManager(self.config)
self.assertFalse(exists(self.txtfile))
with seqinfo.acquire_lock(block_minutes=0):
self.assertTrue(seqinfo._have_lock)
self.assertTrue(exists(self.lockfile))
self.assertFalse(exists(self.txtfile))
self.assertFalse(exists(self.lockfile))
self.assertTrue(exists(self.txtfile))
self.assertFilesEqual(seqinfo.file, self.snapshot)
self.assertFilesEqual(self.txtfile, self.txtsnapshot)
def main():
global LOOPING
try:
special = [int(arg) for arg in sys.argv[1:]]
except ValueError:
print('Error: Args are sequences to be run')
sys.exit(-1)
if special:
LOOPING = False
# de-duplicate while preserving order
seen = set()
seen_add = seen.add # more efficient, tho gain is negligible for small specials
special = [s for s in special if not (s in seen or seen_add(s))]
else:
special = None
seqinfo = SequencesManager(CONFIG)
updater = AllSeqUpdater(CONFIG['AllSeqUpdater'])
# This means you can start it once and leave it, but by setting LOOPING = False you can make it one-and-done
# This would be a good place for a do...while syntax
while True:
quitting = inner_main(updater, seqinfo, special)
if LOOPING and not quitting:
LOGGER.info('Sleeping.')
sleep(SLEEPMINUTES * 60)
else:
break
def test_manual_lock_unlock(self):
seqinfo = SequencesManager(self.config)
seqinfo.lock_read_init()
self.assertTrue(seqinfo._have_lock)
self.assertTrue(exists(self.lockfile))
self.assertFalse(exists(self.txtfile))
seqinfo.write_unlock()
self.assertFalse(exists(self.lockfile))
self.assertTrue(exists(self.txtfile))
self.assertFilesEqual(seqinfo.file, self.snapshot)
self.assertFilesEqual(self.txtfile, self.txtsnapshot)
def test_readonly(self):
seqinfo = SequencesManager(self.config)
seqinfo.readonly_init()
self.assertFalse(seqinfo._have_lock)
self.assertFalse(exists(self.lockfile))
self.assertRaises(LockError, seqinfo.write)
self.assertRaises(LockError, seqinfo.drop, 276)
self.assertRaises(LockError, seqinfo.push_new_info, SequenceInfo)
self.assertRaises(LockError, seqinfo.find_and_drop_merges)
self.assertRaises(LockError, seqinfo.reserve_seqs, 'mersenneforum',
[276])
self.assertRaises(LockError, seqinfo.unreserve_seqs, 'mersenneforum',
[276])
self.assertFalse(exists(self.txtfile))
seqinfo.lock_read_init(
) # Just verify that we can re-init as we please
seqinfo.readonly_init() # ...and that re-init clears all locking state
self.assertFalse(seqinfo._have_lock)
def test_readonly(self):
seqinfo = SequencesManager(self.config)
seqinfo.readonly_init()
self.assertFalse(seqinfo._have_lock)
self.assertFalse(exists(self.lockfile))
self.assertRaises(LockError, seqinfo.write)
self.assertRaises(LockError, seqinfo.drop, 276)
self.assertRaises(LockError, seqinfo.push_new_info, SequenceInfo)
self.assertRaises(LockError, seqinfo.find_and_drop_merges)
self.assertRaises(LockError, seqinfo.reserve_seqs, 'mersenneforum', [276])
self.assertRaises(LockError, seqinfo.unreserve_seqs, 'mersenneforum', [276])
self.assertFalse(exists(self.txtfile))
seqinfo.lock_read_init() # Just verify that we can re-init as we please
seqinfo.readonly_init() # ...and that re-init clears all locking state
self.assertFalse(seqinfo._have_lock)
def test_manual_lock_unlock(self):
seqinfo = SequencesManager(self.config)
seqinfo.lock_read_init()
self.assertTrue(seqinfo._have_lock)
self.assertTrue(exists(self.lockfile))
self.assertFalse(exists(self.txtfile))
seqinfo.write_unlock()
self.assertFalse(exists(self.lockfile))
self.assertTrue(exists(self.txtfile))
self.assertFilesEqual(seqinfo.file, self.snapshot)
self.assertFilesEqual(self.txtfile, self.txtsnapshot)
def main():
seqinfo = SequencesManager(CONFIG)
with seqinfo.acquire_lock(block_minutes=CONFIG['blockminutes']):
LOGGER.info("seqinfo inited, updating priorities...")
for ali in seqinfo.values():
ali.calculate_priority()
def test_already_locked(self):
open(self.lockfile, 'w').close()
seqinfo = SequencesManager(self.config)
self.assertRaises(LockError, seqinfo.lock_read_init)
def main():
seqinfo = SequencesManager(CONFIG)
with seqinfo.acquire_lock(block_minutes=CONFIG['blockminutes']):
LOGGER.info("seqinfo inited, updating priorities...")
for ali in seqinfo.values():
ali.calculate_priority()