def __init__(self, dir):
self.dir = dir
self.files = dict()
for best in glam2.best_files(dir):
fragment, cross_fold_index, seed = glam2.interpret_output_filename(
best)
self.files[(fragment, cross_fold_index)] = best
def worker():
while True:
if options.glam2_format:
pssm_file = q.get()
fragment, fold, seed = glam2.interpret_output_filename(pssm_file)
else:
fragment, fold = q.get()
pssm_file = os.path.join(options.pssm_dir, "%s-%d.pssm" % (fragment, fold))
try:
def execute(args):
logging.info("Executing: %s", " ".join(args))
subprocess.check_call(args)
logging.info("Scoring output: %s: %s, %d", pssm_file, fragment, fold)
script_dir = os.path.dirname(__file__)
args = [
"python2.5",
os.path.join(script_dir, "test_score_pssm.py"),
"-q",
"-d",
harness.options.data_dir, # where sequences are stored
"-r",
options.results_dir, # where to put output
method,
pssm_file,
fragment,
str(fold),
]
if options.glam2_format:
args.append("--glam2-format")
# do positive dataset
execute(args)
# do negative datasets
args.append(None)
for bg in harness.options.backgrounds:
args[-1] = bg
execute(args)
except:
type, value, traceback = sys.exc_info()
logging.exception("Exception (%s) caught: %s", type, value)
sys.exc_clear()
q.task_done()
def worker():
while True:
if options.glam2_format:
pssm_file = q.get()
fragment, fold, seed = glam2.interpret_output_filename(pssm_file)
else:
fragment, fold = q.get()
pssm_file = os.path.join(options.pssm_dir, '%s-%d.pssm' % (fragment, fold))
try:
def execute(args):
logging.info('Executing: %s', ' '.join(args))
subprocess.check_call(args)
logging.info('Scoring output: %s: %s, %d', pssm_file, fragment, fold)
script_dir = os.path.dirname(__file__)
args = [
'python2.5',
os.path.join(script_dir, 'test_score_pssm.py'),
'-q',
'-d', harness.options.data_dir, # where sequences are stored
'-r', options.results_dir, # where to put output
method,
pssm_file,
fragment,
str(fold)
]
if options.glam2_format:
args.append('--glam2-format')
# do positive dataset
execute(args)
# do negative datasets
args.append(None)
for bg in harness.options.backgrounds:
args[-1] = bg
execute(args)
except:
type, value, traceback = sys.exc_info()
logging.exception('Exception (%s) caught: %s', type, value)
sys.exc_clear()
q.task_done()
def __init__(self, dir):
self.dir = dir
self.files = dict()
for best in glam2.best_files(dir):
fragment, cross_fold_index, seed = glam2.interpret_output_filename(best)
self.files[(fragment, cross_fold_index)] = best