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