tcrsampler 0.1.9

Sample TCRs according to VJ gene usage frequency

tcrsampler

Sample TCRs according to VDJ gene usage frequency

Install

pip install tcrsampler

Example

import os
import pandas as pd
from tcrsampler.sampler import TCRsampler
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, use_frequency = True)
t.sample([['TRBV9*01','TRBJ2-7*01', 2],['TRBV7-7*01', 'TRBJ2-4*01', 4] ], depth = 1, use_frequency = True)

[['CASSRTGSLADEQYF', 'CASSATGVVSAQYF'],
 ['CASSLGQAARGIQYF', 'CASSLGQAARGIQYF', 'CASSLGQAARGIQYF', 'CASSLGQAARGIQYF']]

Download Default Background

python -c "from tcrsampler.setup_db import install_all_next_gen; install_all_next_gen(dry_run = False)"