def root_folder(self, create=True):
# NB: used to use a paths string here, see yakir's code for reference
# folder = '{}/{}/'.format(self.dataset.name, self.name)
folder = '{}{}/{}/'.format(paths.simsumstats, self.name, self.arrayind)
if create:
fs.makedir(folder)
return folder
def declare_baseline_preprocessing_in_progress(self):
fs.makedir(self.baseline_path())
def outfile_path(batch_num):
path = s.root_folder() + 'logs/'
fs.makedir(path)
return path + '{}-batch{}.out'.format(self.fsid(), batch_num)
from __future__ import print_function, division
import pyutils.fs as fs
from primitives import *
d = Dataset('GERAhg19')
for nk in [2,3,4,8,10]:
ai = d.random_indivs_df(nk * 1000)
print(len(ai))
dir_name = '/groups/price/yakir/data/datasets/' + d.name + '_ref' + str(nk) + 'k'
fs.makedir(dir_name)
ai.to_csv(dir_name + '/indivs_fam', index=False, header=False, sep='\t')
def beta_folder(self, beta_num, create=True):
folder = '{}{}/'.format(self.root_folder(), beta_num)
if create:
fs.makedir(folder)
return folder
def root_folder(self, create=True):
folder = '{}{}/{}/'.format(paths.simsumstats,
self.dataset.name, self.name)
if create:
fs.makedir(folder)
return folder
def results_folder(self, create=True):
path = paths.results + self.name + '/'
if create:
fs.makedir(path)
return path
def beta_folder(self, beta_num, create=True):
folder = '{}{}/'.format(self.root_folder(), beta_num)
if create:
fs.makedir(folder)
return folder
def root_folder(self, create=True):
folder = '{}{}/{}/'.format(paths.simsumstats, self.dataset.name,
self.name)
if create:
fs.makedir(folder)
return folder
def declare_baseline_preprocessing_in_progress(self):
fs.makedir(self.baseline_path())
def path_to_beta(self, beta_num, create=True):
path = self.path(create=create) + 'beta.' + str(beta_num) + '/'
if create:
fs.makedir(path)
return path
def path(self, create=True):
path = self.path_to_genotypes() + self.name + '/'
if create:
fs.makedir(path)
return path
def path_to_preprocessed_data(self, create=True):
path = self.refpanel.path + self.preprocessing_foldername() + '/'
if create:
fs.makedir(path)
return path
def outfile_path(self, sim, batch_num):
path = sim.path() + 'logs/'
fs.makedir(path)
return path + '{}.batch.{}.out'.format(self.readable_name(), batch_num)
def declare_invcovariance_preprocessing_in_progress(self):
fs.makedir(self.invcovariance_path())
def declare_invcovariance_preprocessing_in_progress(self):
fs.makedir(self.invcovariance_path())
