Metadata-Version: 2.1
Name: tcrsampler
Version: 0.1.2
Summary: Sample TCRs according to VDJ gene usage frequency
Home-page: https://github.com/kmayerb/tcrsampler
Author: Koshlan Mayer-Blackwell
Author-email: kmayerbl@fredhutch.org
Maintainer: Koshlan Mayer-Blackwell
Maintainer-email: kmayerbl@fredhutch.org
License: MIT
Platform: UNKNOWN
Description-Content-Type: text/markdown
Requires-Dist: numpy (>=1.18.1)
Requires-Dist: pandas (>=0.24.2)
Requires-Dist: progress (>=1.5)

# tcrsampler

Sample TCRs according to VDJ gene usage frequency

[![Build Status](https://travis-ci.com/kmayerb/tcrsampler.svg?branch=master)](https://travis-ci.com/kmayerb/tcrsampler)
[![Coverage Status](https://coveralls.io/repos/github/kmayerb/tcrsampler/badge.svg?branch=master)](https://coveralls.io/github/kmayerb/tcrsampler?branch=master)
[![PyPI version](https://badge.fury.io/py/tcrsampler.svg)](https://badge.fury.io/py/tcrsampler)

## Install 

```
pip install tcrsampler
```

### Example

```python
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()
t.sample([['TRBV9*01','TRBJ2-7*01', 2],['TRBV7-7*01', 'TRBJ2-4*01', 4] ], depth = 1)
```

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

### Change depth of sampling

```python
r = t.sample([['TRBV9*01','TRBJ2-7*01', 2],depth = 2)
```

```
[['CASSRTGSLADEQYF', 'CASSATGVVSAQYF', 'CASSAWGQVYEQYF', 'CASSVSGSPYEQYF']]
```


### Change seed

```python
t.sample([['TRBV9*01','TRBJ2-7*01', 2]], depth = 2, seed = 5)
```

```
[['CASRWGEQYF', 'CASSVAEGGPYEQYF', 'CASRWGEQYF', 'CASSSRTSPSYEQYF']]
```

```python
t.sample([['TRBV9*01','TRBJ2-7*01', 2]], depth = 2, seed = 10)
```

```
[['CASSTGTTSYEQYF', 'CASSAWGQVYEQYF', 'CASNPGGRAYEQYF', 'CASSVSGGSYEQYF']]
```

