def sites_to_ids(self):
if self.args.ids_to_sites:
f = self.args.ids_to_sites
else:
f = self.config['ids_to_sites']
sites_to_ids = dict()
for site_id, site in csv_file_reader(f, delimiter='\t'):
sites_to_ids[site] = int(site_id)
return sites_to_ids
def data(self):
d = dict()
for site, bool_ in csv_file_reader(self.fname):
if bool_ == 'True':
bool_ = True
else:
bool_ = False
d[site] = bool_
return d
def ids_to_samples(self):
if self.args.samples:
directory = self.args.samples
else:
directory = self.config['samples']
if os.path.isfile(directory):
files = [directory, ]
else:
files = []
make_abs = functools.partial(os.path.join, directory)
for path in imap(make_abs, os.listdir(directory)):
if os.path.isfile(path):
files.append(path)
samples = dict()
for f in files:
for site, tstamp, code in csv_file_reader(f, delimiter='\t'):
tstamp = parse_tstamp(tstamp)
site_id = self.sites_to_ids[site]
samples[site_id] = (site, tstamp, code)
return samples
