def test_LastProteinIds9(self):
"""LastProteinIds9 should give last protein ids in iter"""
result = LastProteinIds9(self.rec)
self.assertEqual(result, ['ece:Z4181', 'ecs:ECs3717', 'cvi:CV2421',\
'sfl:CP0138', 'spt:SPA2730', 'sec:SC2804', 'stm:STM2872'])
#should also work if threshold set
result = LastProteinIds9(self.rec, False, threshold=8e-6)
self.assertEqual(result, ['ece:Z4181', 'ecs:ECs3717', 'cvi:CV2421',\
'sfl:CP0138'])
#should work on multiple records
result = map(LastProteinIds9, PsiBlastQueryFinder(self.rec2))
self.assertEqual(len(result), 2)
self.assertEqual(result[0], ['ece:Z4181', 'ecs:ECs3717', 'cvi:CV2421',\
'sfl:CP0138', 'spt:SPA2730', 'sec:SC2804', 'stm:STM2872'])
self.assertEqual(result[1], ['ece:Z4182', 'ecs:ECs3718', 'cvi:CV2422'])
def ids_from_seq_lower_threshold(seq, n, max_iterations, app, core_threshold, \
lower_threshold, step=100):
"""Returns ids that match a seq, decreasing the sensitivity."""
last_num_ids = None
checkpoints = []
cp_name_base = make_unique_str()
# cache ides for each iteration
# store { iteration_num:(core_threshold, [list of matching ids]) }
all_ids = {}
try:
i = 0
while 1:
#-h is the e-value threshold for inclusion in the score matrix model
app.Parameters['-h'].on(core_threshold)
app.Parameters['-e'].on(core_threshold)
if core_threshold > lower_threshold:
raise ThresholdFound
if checkpoints:
#-R restarts from a previously stored file
app.Parameters['-R'].on(checkpoints[-1])
#store the score model from this iteration
curr_check = 'checkpoint_' + cp_name_base + '_' + str(i) + \
'.chk'
app.Parameters['-C'].on(curr_check)
output = app(seq)
result = list(output.get('BlastOut', output['StdOut']))
#sometimes fails on first try -- don't know why, but this seems
#to fix problem
while not result:
output = app(seq)
result = list(output.get('BlastOut', output['StdOut']))
ids = LastProteinIds9(result,
keep_values=True,
filter_identity=False)
output.cleanUp()
all_ids[i + 1] = (core_threshold, copy(ids))
if not access(curr_check, F_OK):
raise ThresholdFound
checkpoints.append(curr_check)
num_ids = len(ids)
if num_ids >= n:
raise ThresholdFound
last_num_ids = num_ids
core_threshold *= step
if i >= max_iterations - 1: #because max_iterations is 1-based
raise ThresholdFound
i += 1
except ThresholdFound:
for c in checkpoints:
remove(c)
#turn app.Parameters['-R'] off so that for the next file it does not
#try and read in a checkpoint file that is not there
app.Parameters['-R'].off()
return ids, i + 1, all_ids
def ids_from_seq_two_step(seq, n, max_iterations, app, core_threshold, \
extra_threshold, lower_threshold, second_db=None):
"""Returns ids that match a seq, using a 2-tiered strategy.
Optionally uses a second database for the second search.
"""
#first time through: reset 'h' and 'e' to core
#-h is the e-value threshold for including seqs in the score matrix model
app.Parameters['-h'].on(core_threshold)
#-e is the e-value threshold for the final blast
app.Parameters['-e'].on(core_threshold)
checkpoints = []
ids = []
last_num_ids = None
for i in range(max_iterations):
if checkpoints:
app.Parameters['-R'].on(checkpoints[-1])
curr_check = 'checkpoint_%s.chk' % i
app.Parameters['-C'].on(curr_check)
output = app(seq)
#if we didn't write a checkpoint, bail out
if not access(curr_check, F_OK):
break
#if we got here, we wrote a checkpoint file
checkpoints.append(curr_check)
result = list(output.get('BlastOut', output['StdOut']))
output.cleanUp()
if result:
ids = LastProteinIds9(result,
keep_values=True,
filter_identity=False)
num_ids = len(ids)
if num_ids >= n:
break
if num_ids == last_num_ids:
break
last_num_ids = num_ids
#if we didn't write any checkpoints, second run won't work, so return ids
if not checkpoints:
return ids
#if we got too many ids and don't have a second database, return the ids we got
if (not second_db) and num_ids >= n:
return ids
#second time through: reset 'h' and 'e' to get extra hits, and switch the
#database if appropriate
app.Parameters['-h'].on(extra_threshold)
app.Parameters['-e'].on(lower_threshold)
if second_db:
app.Parameters['-d'].on(second_db)
for i in range(
max_iterations): #will always have last_check if we get here
app.Parameters['-R'].on(checkpoints[-1])
curr_check = 'checkpoint_b_%s.chk' % i
app.Parameters['-C'].on(curr_check)
output = app(seq)
#bail out if we couldn't write a checkpoint
if not access(curr_check, F_OK):
break
#if we got here, the checkpoint worked
checkpoints.append(curr_check)
result = list(output.get('BlastOut', output['StdOut']))
if result:
ids = LastProteinIds9(result,
keep_values=True,
filter_identity=False)
num_ids = len(ids)
if num_ids >= n:
break
if num_ids == last_num_ids:
break
last_num_ids = num_ids
#return the ids we got. may not be as many as we wanted.
for c in checkpoints:
remove(c)
return ids