Python make_path_dump Examples

Example #1

File: Tests.py Project: anyone1985/TCGA_Working

 def save(self):
     if hasattr(self.test, 'first_pass'):
         del self.test.first_pass
     if hasattr(self.test, 'full_test'):
         del self.test.full_test
     make_path_dump(self, self.path + '/TestResult.p')
     self.results.to_csv(self.path + '/TestResults.csv')

Example #2

File: Containers.py Project: anyone1985/TCGA_Working

 def save(self):
     self.path = '{}/{}'.format(self.run_path, self.cancer)
     make_path_dump(self, self.path + '/Clinical/ClinicalObject.p')
     if type(self.drugs) != type(None):
         self.drugs.to_csv(self.path + '/Clinical/drugs.csv')
     if type(self.survival) != type(None):
         self.survival.to_csv(self.path + '/Clinical/survival.csv')
     self.timeline.to_csv(self.path + '/Clinical/timeline.csv')
     self.clinical.to_csv(self.path + '/Clinical/clinical.csv')

Example #3

 def save(self):
     self.path = '{}/{}'.format(self.run_path, self.cancer)
     make_path_dump(self, self.path + '/Clinical/ClinicalObject.p')
     if self.drugs is not None:
         self.drugs.to_csv(self.path + '/Clinical/drugs.csv')
     if self.survival is not None:
         self.survival.to_csv(self.path + '/Clinical/survival.csv')
     self.timeline.to_csv(self.path + '/Clinical/timeline.csv')
     self.clinical.to_csv(self.path + '/Clinical/clinical.csv')

Example #4

File: InitializeCancer.py Project: anyone1985/TCGA_Working

def initialize_cancer(run, cancer_type, patients=None, filtered_patients=None):
    cancer = Cancer(cancer_type, run)
    cancer.patients = patients
    cancer.filtered_patients = filtered_patients
    cancer.path = '/'.join([run.report_path, cancer.name])
    make_path_dump(cancer, cancer.path + '/CancerObject.p')
    
    clinical = Clinical(cancer, run, patients, filtered_patients)
    clinical.artificially_censor(5)
    make_path_dump(clinical, cancer.path + '/Clinical/ClinicalObject.p')
    if type(clinical.drugs) != type(None):
        clinical.drugs.to_csv(cancer.path + '/Clinical/drugs.csv')
    if type(clinical.survival) != type(None):
        clinical.survival.to_csv(cancer.path + '/Clinical/survival.csv')
    clinical.timeline.to_csv(cancer.path + '/Clinical/timeline.csv')
    clinical.clinical.to_csv(cancer.path + '/Clinical/clinical.csv')
    
    global_vars = get_global_vars(cancer.name, run.data_path, patients, 
                                  filtered_patients)
    global_vars.to_csv(cancer.path + '/Global_Vars.csv')

Example #5

File: Containers.py Project: anyone1985/TCGA_Working

 def save(self):
     self.report_path = (self.result_path + 'Run_' + 
                         self.version.replace('.', '_'))
     make_path_dump(self, self.report_path + '/RunObject.p')

Example #6

File: Containers.py Project: anyone1985/TCGA_Working

 def save(self):
     if self.compressed is False:
         self.compress()
     make_path_dump(self, self.path + '/DataObject.p')

Example #7

File: Containers.py Project: anyone1985/TCGA_Working

 def save(self):
     self.path = '{}/{}'.format(self.run_path, self.name)
     make_path_dump(self, self.path + '/CancerObject.p')        

Example #8

 def save(self):
     self.report_path = (self.result_path + 'Run_' +
                         self.version.replace('.', '_'))
     make_path_dump(self, self.report_path + '/RunObject.p')

Example #9

 def save(self):
     if self.compressed is False:
         self.compress()
     make_path_dump(self, self.path + '/DataObject.p')

Example #10

 def save(self):
     self.path = '{}/{}'.format(self.run_path, self.name)
     make_path_dump(self, self.path + '/CancerObject.p')