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 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())