def load(self, sim_dirname):
if not os.path.isdir(sim_dirname):
raise Exception, "No simulation in %s" %(sim_dirname)
self.name = os.path.basename(sim_dirname)
self.sim_dirname = sim_dirname
self.run_fname = os.path.join(self.sim_dirname, LAST_RUN_FNAME)
if not os.path.isfile(self.run_fname):
raise Exception, "No run file found for simulation in %s" \
%(sim_dirname)
# load last run time
with open(self.run_fname) as run_f:
self.last_run_time = run_f.readline().strip()
# load parameters
self.params_fname = os.path.join(self.sim_dirname, PARAMS_FNAME)
if not os.path.isfile(self.params_fname):
raise Exception, "No params file found for simulation in %s" \
%(sim_dirname)
with open(self.params_fname) as params_f:
self.params = json.load(params_f)
# load simulation contents
sim_files = glob.glob("%s/*.sim" %(self.sim_dirname))
print "loading simulation (%d files)" %(len(sim_files))
for curr_fname in sim_files:
curr_fname = utils.pathify(curr_fname)
sim_name = os.path.basename(curr_fname).split(".sim")[0]
sim_df = pandas.read_table(curr_fname, sep=self.sep)
self.data[sim_name] = sim_df
def main():
from optparse import OptionParser
parser = OptionParser()
parser.add_option("--compute-qc", dest="compute_qc", nargs=1, default=None,
help="Compute QC metrics for RNA-Seq library. Takes as input a BAM file.")
parser.add_option("--get-cycle-profile", dest="get_cycle_profile", nargs=1, default=None,
help="Get cycle profile for sequence. Takes as input a FASTQ file.")
parser.add_option("--settings", dest="settings", nargs=1, default=None,
help="Settings filename.")
parser.add_option("--output-dir", dest="output_dir", nargs=1, default=None,
help="Output directory.")
(options, args) = parser.parse_args()
output_dir = options.output_dir
if output_dir != None:
output_dir = pathify(output_dir)
if not os.path.isdir(output_dir):
os.makedirs(output_dir)
if options.get_cycle_profile != None:
fastq_filename = utils.pathify(options.get_cycle_profile)
get_cycle_profile(fastq_filename)
def main():
from optparse import OptionParser
parser = OptionParser()
parser.add_option(
"--compute-qc",
dest="compute_qc",
nargs=1,
default=None,
help=
"Compute QC metrics for RNA-Seq library. Takes as input a BAM file.")
parser.add_option(
"--get-cycle-profile",
dest="get_cycle_profile",
nargs=1,
default=None,
help="Get cycle profile for sequence. Takes as input a FASTQ file.")
parser.add_option("--settings",
dest="settings",
nargs=1,
default=None,
help="Settings filename.")
parser.add_option("--output-dir",
dest="output_dir",
nargs=1,
default=None,
help="Output directory.")
(options, args) = parser.parse_args()
output_dir = options.output_dir
if output_dir != None:
output_dir = pathify(output_dir)
if not os.path.isdir(output_dir):
os.makedirs(output_dir)
if options.get_cycle_profile != None:
fastq_filename = utils.pathify(options.get_cycle_profile)
get_cycle_profile(fastq_filename)
import pandas as pd
from utils import pathify
data = pd.read_csv(pathify('data/SICK.txt'), sep='\t')
for dataset in set(data['SemEval_set']):
data[data['SemEval_set'] == dataset].to_csv(pathify(
'data/sick', f'{dataset.lower()}.txt'),
sep='\t')
def __etalon_file__(name, flags):
return os.path.join(
config.get_output(),
"{0}.{1}.etalon".format(name, utils.pathify(flags)))
def worker():
# TODO: clean this up
global _running, initial_get
_running = True
initial_get = True
log.info("Starting read loop")
while _running:
if initial_get:
initial_get = False
netw = {}
fan = {}
co2 = None
humi = None
temp = None
try:
_netw = get_network_data(conn)
cnetw = changes(netw, _netw)
netw = _netw
for (t, v) in pathify(cnetw, "{}/network".format(topic_namespace)):
publish(t, v)
except Exception as e:
log.warn("An exception occured getting network, skipping",
exc_info=True)
try:
_fan = get_fan_speed(conn)
cfan = changes(fan, _fan)
fan = _fan
for (t, v) in pathify(cfan, "{}/fan".format(topic_namespace)):
publish(t, v)
except Exception as e:
log.warn("An exception occured getting fan speed, skipping",
exc_info=True)
try:
_temp = get_temperature(conn)
if _temp != temp:
temp = _temp
publish("{}/temp".format(topic_namespace), temp)
except Exception as e:
log.warn("An exception occured getting temp, skipping",
exc_info=True)
try:
_co2 = get_co2(conn)
if _co2 != co2:
co2 = _co2
publish("{}/co2".format(topic_namespace), co2)
except Exception as e:
log.warn("An exception occured getting CO2, skipping",
exc_info=True)
try:
_humi = get_humidity(conn)
if _humi != humi:
humi = _humi
publish("{}/humi".format(topic_namespace), humi)
except Exception as e:
log.warn("An exception occured getting humidity, skipping",
exc_info=True)
for _ in range(15):
sleep(1)
if not _running:
break
