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)"
1 maintainer
Metadata
1 maintainer
Release files for tcrsampler 0.1.9
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Source distribution (sdist)
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| tcrsampler-0.1.9.tar.gz | 416.0 kB | Details |
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| tcrsampler-0.1.9-py3-none-any.whl | Python 3 | none | any | Details |
Total release size: 854.1 kB
Release files / tcrsampler-0.1.9.tar.gz
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Release files / tcrsampler-0.1.9-py3-none-any.whl
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| Tags | Python 3 |
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