def main(args):
options = parse_args(args)
#Open up connection to database
engine = dbtables.connect(options.db)
Session = sessionmaker(bind=engine)
session = Session()
#Get all of the blanks in groups, as a dictionary by mode. Then compress to a single run
# for each mode. Note: the compound information in compressed runs is not very reliable.
# the adduct information is what is preserved.
blanks = group_cefs(*options.blanks)
for mode in blanks:
for ind, blank in enumerate(blanks[mode]):
blanks[mode][ind] = cefparse.read_cef(blank)
blanks[mode] = btools.comb_runs(20, 0.4, *blanks[mode])
runs = []
ceflists = group_cefs(*options.cefs)
modes = ceflists.keys()
#This is for the parallelization, this says only use this computer, no network cluster
ppservers = ()
if options.cpus:
job_server = pp.Server(options.cpus, ppservers=ppservers, secret='acetone')
else:
job_server = pp.Server(ppservers=ppservers, secret='acetone')
print "Running with ", job_server.get_ncpus(), " CPU's"
widgets = ['Submitting Jobs: ', Percentage(), ' ', Bar(marker=RotatingMarker()), ' ', ETA(),\
' ', FileTransferSpeed()]
pbar = ProgressBar(widgets=widgets, maxval=len(ceflists.values()[0])).start()
for ind, group in enumerate(zip(*ceflists.values())):
if len(group) < 4:
print "Skipping: ", group
continue
small = dict([(mode, cef) for mode, cef in zip(modes, group)])
#Submit the group as a job to parallel process
print group
runs.append(job_server.submit(process, (small, blanks, options.cutoff, options.rt,), (),
("btools", "sys", "re", "cefparse", "sqlalchemy.orm", "sqlalchemy.ext.declarative",
"dbtables", "val",)))
pbar.update(ind + 1)
pbar.finish()
#This portion is for the progress bar.
widgets = ['COMMITING: ', Percentage(), ' ', Bar(marker=RotatingMarker()), ' ', ETA(),\
' ', FileTransferSpeed()]
pbar = ProgressBar(widgets=widgets, maxval=len(runs)).start()
for ind, run in enumerate(runs):
session.add(run())
session.commit()
pbar.update(ind + 1)
pbar.finish()
def __init__(self, db, tabfile, quant=True, remove=True, bqs=['00110', '00100', '10000', '10100', '10110', '11000', '11100', '11110','00111', '00101', '10001', '10101', '10111', '11001', '11101', '11111']): bqs = set(bqs) self.db = db self.engine = dbtables.connect(db) self.Session = sessionmaker(bind=self.engine) self.session = self.Session() self.cp = self.get_cp(tabfile) self.ad_heat = self.get_bins([finger.name for finger in self.cp.fingerprints()], bqs) if remove: self.remove_systematic(0.1) self.remove_underrepresent() if quant: self.quant()
def __init__(self, db, tabfile, quant=True, remove=True, bqs=['00110', '00100', '10000', '10100', '10110', '11000', '11100', '11110','00111', '00101', '10001', '10101', '10111', '11001', '11101', '11111']): bqs = set(bqs) self.db = db self.engine = dbtables.connect(db) self.Session = sessionmaker(bind=self.engine) self.session = self.Session() self.synleth = self.get_synleth(tabfile) self.ad_heat = self.get_bins([str(pref) for pref in self.synleth.prefs], bqs) if remove: self.remove_systematic(0.1) self.remove_underrepresent() if quant: self.quant()
