text: import os
  import pytest
  from biomarker_survival import mutation_base
  from biomarker_survival import TCGA_CDR_util
  
  FIXTURE_DIR = os.path.join(
     os.path.dirname(os.path.realpath(__file__)),
     'test_data',
    )
  
  @pytest.fixture(scope="module")
  def tcga_cdr():
    path = os.path.join(FIXTURE_DIR, 'TCGA-CDR-SupplementalTableS1-2019-05-27.xlsx')
    return TCGA_CDR_util(path)
  
  def test_prep_mutation_data_alone(tcga_cdr):
    path = os.path.join(FIXTURE_DIR, 'mutations-first-thousand-lines-2019-05-19.txt')
  
    muts = mutation_base.prep_mutation_data_alone(path)
    patient_genes = mutation_base.prep_mutation_data(muts, tcga_cdr.cancer_type_data('*'), 'GBM')
    assert list(patient_genes.index)[0] == 'TCGA-02-0003'
    assert patient_genes.columns[0] == '\'ABR'
    assert patient_genes.values.max() == 1
    assert patient_genes.values.min() == 0
  
  
  