def test_ex12():
import pandas as pd
import os
from tcrsampler.sampler import TCRsampler
# fn = 'britanova_chord_blood.csv' # real file
fn = os.path.join('tcrdist','test_files', 'britanova_chord_blood_sample_5000.csv') # test_only file
t = TCRsampler()
t.ref_df = pd.read_csv(fn)
t.build_background()
t.v_freq
t.j_freq
t.vj_freq
t.sample_background(v ='TRBV10-1*01', j ='TRBJ1-1*01',n=3, depth = 1, seed =1, use_frequency= True )
def test_prob_sampler_sample_background():
t = TCRsampler()
fn = os.path.join('tcrsampler', 'tests', 'pmbc_mixcr_example_data.txt')
t.clean_mixcr(filename=fn)
t.build_background()
r = t.sample_background('TRBV9*01', 'TRBJ2-7*01', n=10)
assert r == [
'CASSRTGSLADEQYF', 'CASSATGVVSAQYF', 'CASSAWGQVYEQYF',
'CASSVSGSPYEQYF', 'CASSAWGQVYEQYF', 'CASSAWGQVYEQYF', 'CASRWGEQYF',
'CASSGDDWEQYF', 'CASSATGTSGPYEQYF', 'CASSSRTSGSNSEQYF'
]
def test_TCRsampler_build_stratified():
t = TCRsampler()
fn = os.path.join('tcrsampler', 'tests', 'pmbc_mixcr_example_data.txt')
t.clean_mixcr(filename=fn)
t.build_background(stratify_by_subject=True)
r = t.sample_background('TRBV9*01', 'TRBJ2-7*01', n=10)